diff --git a/src/3rd_party/3rd_party_clean.c b/src/3rd_party/3rd_party_clean.c
index b5e3459c..1b8ba901 100644
--- a/src/3rd_party/3rd_party_clean.c
+++ b/src/3rd_party/3rd_party_clean.c
@@ -95,14 +95,23 @@ static enum swupd_code clean_repos_state(UNUSED_PARAM char *unused)
 {
 	enum swupd_code ret;
 	int files_removed;
+	size_t bytes_removed;
+	char *bytes_removed_pretty = NULL;
 
-	ret = clean_statedir(cmdline_option_dry_run, cmdline_option_all);
-	files_removed = clean_get_stats();
+	clean_reset_stats();
+	ret = clean_cachedir();
+
+	files_removed = clean_get_file_stats();
+	bytes_removed = clean_get_byte_stats();
+	prettify_size(bytes_removed, &bytes_removed_pretty);
 	if (cmdline_option_dry_run) {
 		info("Would remove %d files\n", files_removed);
+		info("Aproximatelly %s would be freed\n", bytes_removed_pretty);
 	} else {
 		info("%d files removed\n", files_removed);
+		info("%s freed\n", bytes_removed_pretty);
 	}
+	FREE(bytes_removed_pretty);
 
 	return ret;
 }
@@ -124,6 +133,10 @@ enum swupd_code third_party_clean_main(int argc, char **argv)
 		return ret_code;
 	}
 
+	/* set the command options */
+	clean_set_option_all(cmdline_option_all);
+	clean_set_option_dry_run(cmdline_option_dry_run);
+
 	/* clean the cache */
 	ret_code = third_party_run_operation_multirepo(cmdline_option_repo, clean_repos_state, SWUPD_OK, "clean", steps_in_clean);
 
diff --git a/src/cmds/clean.c b/src/cmds/clean.c
index f060dcfd..bc1362c3 100644
--- a/src/cmds/clean.c
+++ b/src/cmds/clean.c
@@ -19,6 +19,7 @@
 
 #include <ctype.h>
 #include <errno.h>
+#include <ftw.h>
 #include <getopt.h>
 #include <sys/stat.h>
 #include <time.h>
@@ -29,6 +30,42 @@
 #define FLAG_ALL 2000
 #define FLAG_DRY_RUN 2001
 
+static struct {
+	int all;
+	int dry_run;
+} options;
+
+static struct {
+	int files_removed;
+	size_t bytes_removed;
+} stats;
+
+void clean_set_option_all(bool opt)
+{
+	options.all = opt;
+}
+
+void clean_set_option_dry_run(bool opt)
+{
+	options.dry_run = opt;
+}
+
+int clean_get_file_stats(void)
+{
+	return stats.files_removed;
+}
+
+size_t clean_get_byte_stats(void)
+{
+	return stats.bytes_removed;
+}
+
+void clean_reset_stats(void)
+{
+	stats.files_removed = 0;
+	stats.bytes_removed = 0;
+}
+
 static void print_help(void)
 {
 	print("Remove cached content used for updates from state directory\n\n");
@@ -44,21 +81,6 @@ static void print_help(void)
 	    "\n");
 }
 
-static struct {
-	int all;
-	int dry_run;
-} options;
-
-static struct {
-	int files_removed;
-	size_t bytes_removed;
-} stats;
-
-int clean_get_stats(void)
-{
-	return stats.files_removed;
-}
-
 static const struct option prog_opts[] = {
 	{ "help", no_argument, 0, 'h' },
 	{ "all", no_argument, 0, FLAG_ALL },
@@ -181,11 +203,6 @@ static enum swupd_code remove_if(const char *path, bool dry_run, remove_predicat
 	return ret;
 }
 
-static bool is_fullfile(const char UNUSED_PARAM *dir, const struct dirent *entry)
-{
-	return str_len(entry->d_name) == (SWUPD_HASH_LEN - 1);
-}
-
 static bool is_pack_indicator(const char UNUSED_PARAM *dir, const struct dirent *entry)
 {
 	static const char prefix[] = "pack-";
@@ -361,7 +378,15 @@ static enum swupd_code clean_staged_manifests(const char *path, bool dry_run, bo
 		if (size < 0) {
 			size = 0;
 		}
+
+		// when doing a dry run, if --all was selcted we can assume the
+		// directory will also get deleted since it should be empty by now
+		if (dry_run && all) {
+			print("%s\n", version_dir);
+		}
+
 		if (!rmdir(version_dir) || (dry_run && all)) {
+			stats.files_removed++;
 			stats.bytes_removed += long_to_ulong(size);
 		}
 
@@ -405,7 +430,7 @@ enum swupd_code clean_main(int argc, char **argv)
 	 * and keeping all the staged files of the current version. This helps recovering the
 	 * current version. Or do it for the previous version to allow a rollback. */
 
-	ret = clean_statedir(options.dry_run, options.all);
+	ret = clean_cachedir();
 
 	/* TODO: Also print the bytes removed, need to take into account the hardlinks. */
 	prettify_size(stats.bytes_removed, &bytes_removed_pretty);
@@ -424,49 +449,251 @@ enum swupd_code clean_main(int argc, char **argv)
 	return ret;
 }
 
-/* clean_statedir will clean the state directory used by swupd (default to
- * /var/lib/swupd). It will remove all files except relevant manifests unless
- * all is set to true. Setting dry_run to true will print the files that would
- * be removed but will not actually remove them. */
-enum swupd_code clean_statedir(bool dry_run, bool all)
+static int remove_irrelevant_file(const char *filename, const struct stat *st, int type __attribute__((unused)), struct FTW *ftw __attribute__((unused)))
+{
+	int ret;
+	char *root_cache_path = NULL;
+	char *relevant_path = NULL;
+
+	// skip the starting directory of the walk
+	root_cache_path = statedir_get_cache_dir();
+	ret = strncmp(filename, root_cache_path, str_len(filename));
+	FREE(root_cache_path);
+	if (ret == 0) {
+		return 0;
+	}
+
+	// if the file is from the current mirror, it
+	// is still relevant, skip it
+	relevant_path = statedir_get_cache_url_dir();
+	ret = str_starts_with(filename, relevant_path);
+	FREE(relevant_path);
+	if (ret == 0){
+		return 0;
+	}
+
+	// if we got here, the file is irrelevant to the current mirror
+	if (options.dry_run) {
+		print("%s\n", filename);
+	} else {
+		ret = sys_rm(filename);
+		if (ret) {
+			return ret;
+		}
+	}
+	stats.files_removed++;
+	stats.bytes_removed+=long_to_ulong(st->st_size);
+
+	return 0;
+}
+
+static int count_file(const char *filename, const struct stat *st, int type __attribute__((unused)), struct FTW *ftw __attribute__((unused)))
+{
+	if (options.dry_run) {
+		print("%s\n", filename);
+	}
+	stats.files_removed++;
+	stats.bytes_removed+=long_to_ulong(st->st_size);
+
+	return 0;
+}
+
+static enum swupd_code count_dir_contents(const char *path)
+{
+	int ret;
+
+	ret = nftw(path, &count_file, 0, FTW_DEPTH | FTW_PHYS | FTW_MOUNT);
+	if (ret) {
+		return SWUPD_COULDNT_REMOVE_FILE;
+	}
+
+	return SWUPD_OK;
+}
+
+static enum swupd_code clean_irrelevant_cache(void)
+{
+	int ret;
+	char *dir = NULL;
+
+	dir = statedir_get_cache_dir();
+	ret = nftw(dir, &remove_irrelevant_file, 0, FTW_DEPTH | FTW_PHYS | FTW_MOUNT);
+	FREE(dir);
+	if (ret) {
+		if (errno == ENOENT) {
+			return SWUPD_COULDNT_LIST_DIR;
+		} else {
+			return SWUPD_OUT_OF_MEMORY_ERROR;
+		}
+	}
+
+	return SWUPD_OK;
+}
+
+static enum swupd_code remove_cache_directory(const char *dir)
+{
+	enum swupd_code ret_code;
+	int ret;
+
+	if (!sys_is_dir(dir)){
+		return SWUPD_OK;
+	}
+
+	ret_code = count_dir_contents(dir);
+	if (ret_code) {
+		return ret_code;
+	}
+
+	if (!options.dry_run) {
+		ret = sys_rm_recursive(dir);
+		if (ret < 0 && ret != -ENOENT) {
+			return SWUPD_COULDNT_REMOVE_FILE;
+		}
+	}
+
+	return SWUPD_OK;
+}
+
+/* TODO: Remove after format bump to format 31
+ * clean_statedir will clean the old statedir location used by swupd.
+ */
+static enum swupd_code clean_former_statedir(void)
 {
 	enum swupd_code ret;
 	char *path = NULL;
 
-	path = statedir_get_staged_dir();
-	ret = remove_if(path, dry_run, is_fullfile);
-	FREE(path);
-	if (ret != SWUPD_OK) {
-		return ret;
-	}
-
 	/* Pack presence indicator files. */
-	path = statedir_get_delta_pack_dir();
-	ret = remove_if(path, dry_run, is_pack_indicator);
-	FREE(path);
+	ret = remove_if(globals.cache_dir, options.dry_run, is_pack_indicator);
 	if (ret != SWUPD_OK) {
 		return ret;
 	}
 
 	/* Manifest delta files. */
-	path = statedir_get_manifest_delta_dir();
-	ret = remove_if(path, dry_run, is_manifest_delta);
+	ret = remove_if(globals.cache_dir, options.dry_run, is_manifest_delta);
+	if (ret != SWUPD_OK) {
+		return ret;
+	}
+
+	path = sys_path_join("%s/%s", globals.cache_dir, "staged");
+	ret = remove_cache_directory(path);
 	FREE(path);
 	if (ret != SWUPD_OK) {
 		return ret;
 	}
 
-	/* NOTE: do not clean the state_dir/bundles directory */
-	path = statedir_get_manifest_root_dir();
-	ret = clean_staged_manifests(path, dry_run, all);
+	path = sys_path_join("%s/%s", globals.cache_dir, "manifest");
+	ret = remove_cache_directory(path);
 	FREE(path);
 	if (ret != SWUPD_OK) {
 		return ret;
 	}
 
-	// TODO: Remove after format bump to format 31
-	// Clean all manifests outside of the new manifests folder
-	ret = clean_staged_manifests(globals.cache_dir, dry_run, true);
+	path = sys_path_join("%s/%s", globals.cache_dir, "delta");
+	ret = remove_cache_directory(path);
+	FREE(path);
+	if (ret != SWUPD_OK) {
+		return ret;
+	}
+
+	path = sys_path_join("%s/%s", globals.cache_dir, "download");
+	ret = remove_cache_directory(path);
+	FREE(path);
+	if (ret != SWUPD_OK) {
+		return ret;
+	}
+
+	// Manifest files from old location.
+	ret = clean_staged_manifests(globals.cache_dir, options.dry_run, true);
 
 	return ret;
 }
+
+/* clean_cachedir will clean the cache directory used by swupd (default to
+ * /var/lib/swupd/cache). It will remove all files except relevant manifests from
+ * the cache asociated to the current mirror being used unless all is set to true.
+ * Setting options.dry_run to true will print the files that would be removed but
+ * will not actually remove them. */
+enum swupd_code clean_cachedir(void)
+{
+	enum swupd_code ret_code = SWUPD_OK;
+	char *dir = NULL;
+
+	if (options.all) {
+		// remove the whole cache directory, it will be regenerated
+		// from scratch the next time swupd initializes
+		dir = statedir_get_cache_dir();
+		ret_code = remove_cache_directory(dir);
+		FREE(dir);
+		if (ret_code) {
+			return ret_code;
+		}
+	} else {
+		// remove everything from the cache directory except
+		// relevant manifests
+		dir = statedir_get_cache_url_dir();
+		ret_code = remove_if(dir, options.dry_run, is_pack_indicator);
+		FREE(dir);
+		if (ret_code) {
+			return ret_code;
+		}
+
+		dir = statedir_get_delta_dir();
+		ret_code = remove_cache_directory(dir);
+		FREE(dir);
+		if (ret_code) {
+			return ret_code;
+		}
+
+		dir = statedir_get_download_dir();
+		ret_code = remove_cache_directory(dir);
+		FREE(dir);
+		if (ret_code) {
+			return ret_code;
+		}
+
+		dir = statedir_get_staged_dir();
+		ret_code = remove_cache_directory(dir);
+		FREE(dir);
+		if (ret_code) {
+			return ret_code;
+		}
+
+		dir = statedir_get_temp_dir();
+		ret_code = remove_cache_directory(dir);
+		FREE(dir);
+		if (ret_code) {
+			return ret_code;
+		}
+
+		// clean manifests that are not relevant to the current version
+		// these include:
+		// - manifests from very old versions (versions no longer included in the current mom)
+		// - manifests from versions newer than the current version
+		// - manifests with hashes (e.g. Manifest.vim.<manifest_hash>)
+		dir = statedir_get_manifest_root_dir();
+		/* Manifest delta files. */
+		ret_code = remove_if(dir, options.dry_run, is_manifest_delta);
+		if (ret_code != SWUPD_OK) {
+			FREE(dir);
+			return ret_code;
+		}
+		ret_code = clean_staged_manifests(dir, options.dry_run, false);
+		FREE(dir);
+		if(ret_code) {
+			return ret_code;
+		}
+
+		// remove all cache from other mirror URLs
+		ret_code = clean_irrelevant_cache();
+		if(ret_code) {
+			return ret_code;
+		}
+	}
+
+	// TODO: Remove after format bump to format 31
+	// We need to clean everything in the old statedir locations
+	// regardless of if --all was used, manifests in old locations
+	// will no longer be used
+	ret_code = clean_former_statedir();
+
+	return ret_code;
+}
diff --git a/src/cmds/update.c b/src/cmds/update.c
index ff90f4ab..b5d9c46e 100644
--- a/src/cmds/update.c
+++ b/src/cmds/update.c
@@ -504,7 +504,7 @@ clean_curl:
 	/* clean up our cached content from the update. It is likely much more than
 	 * we need and the clean helps us prevent cache bloat. */
 	if (!keepcache) {
-		clean_statedir(false, false);
+		clean_cachedir();
 	}
 	free_subscriptions(&latest_subs);
 
diff --git a/src/swupd.h b/src/swupd.h
index 49eb8ad5..57c76a58 100644
--- a/src/swupd.h
+++ b/src/swupd.h
@@ -369,7 +369,12 @@ extern void bundle_list_set_option_status(bool opt);
 extern void bundle_list_set_option_orphans(bool opt);
 
 /* clean.c */
-extern int clean_get_stats(void);
+extern void clean_set_option_all(bool opt);
+extern void clean_set_option_dry_run(bool opt);
+extern int clean_get_file_stats(void);
+extern size_t clean_get_byte_stats(void);
+extern void clean_reset_stats(void);
+extern enum swupd_code clean_cachedir(void);
 
 /* 3rd_party_check_update.c */
 enum swupd_code third_party_execute_check_update(void);
@@ -384,8 +389,6 @@ extern enum swupd_code print_update_conf_info(void);
 
 extern int handle_mirror_if_stale(void);
 
-extern enum swupd_code clean_statedir(bool all, bool dry_run);
-
 extern void warn_nosigcheck(const char *file);
 
 /* Parameter parsing in global.c */
diff --git a/test/functional/3rd-party/3rd-party-clean.bats b/test/functional/3rd-party/3rd-party-clean.bats
new file mode 100755
index 00000000..ecbc0b72
--- /dev/null
+++ b/test/functional/3rd-party/3rd-party-clean.bats
@@ -0,0 +1,235 @@
+#!/usr/bin/env bats
+
+# Author: Castulo Martinez
+# Email: castulo.martinez@intel.com
+
+load "../testlib"
+
+test_setup() {
+
+	create_test_environment "$TEST_NAME"
+	set_current_version "$TEST_NAME" 33000
+
+	# ######################################################################
+	# cache/data structure post swupd 4.2.1 (split cache/data) for 3rd-party
+	# ######################################################################
+	# <cachedir>
+	# └── 3rd-party
+	#	  └── cache
+	#	      ├── repo1
+	#	      │   ├── delta
+	#	      │   ├── download
+	#	      │   ├── manifest
+	#	      │   │   ├── 10
+	#	      │   │   │   ├── Manifest.p11-kit
+	#	      │   │   │   └── Manifest.p11-kit.dfd541b1ac9256982044848f2128f51e23ddbb72f68e9de43adaf8f7ead93657
+	#	      │   │   ├── 20
+	#	      │   │   │   ├── Manifest.MoM
+	#	      │   │   │   ├── Manifest.MoM.sig
+	#	      │   │   │   ├── Manifest.emacs
+	#	      │   │   │   └── Manifest.emacs.7414710480607fa89c307ad11d145d8bb0cbdbdf3c0692f940d906b670f6fd5d
+	#	      │   │   ├── Manifest-emacs-delta-from-10-to-20
+	#	      │   │   └── Manifest-vim-delta-from-10-to-20
+	#	      │   ├── pack-blender-from-0-to-20.tar
+	# 	      │   ├── pack-vim-from-10-to-20.tar
+	# 	      │   ├── staged
+	# 	      │   │   ├── 00004ead4b4eb1cef1ebbe13849f6c47c21d325182f98cf8f5333e9a76d2e2df
+	# 	 	  │   │   └── fffe891980af628e498b16a364b5b4d00377485370ccc4d09ac0fc072e85b31d
+	#         │   └── temp
+	# 	      └── repo2
+	#  	          ├── delta
+	#             ├── download
+	#	          ├── manifest
+	#	          │   ├── 50
+	#	          │   │   ├── Manifest.MoM
+	#	          │   │   └── Manifest.MoM.sig
+	#	          │   └── Manifest-qt-basic-delta-from-40-to-50
+	#	          ├── pack-lib-imageformat-from-30-to-50.tar
+	#	          ├── staged
+	#	  	      │   └── ffaf66dab58a2074e5fe9dc6ab7bf8773c069817dcccf631148b6afc87166b4b
+	#             └── temp
+
+	# <datadir>
+	# └── 3rd-party
+	#	  ├── bundles
+	#	  │   ├── editors
+	#	  │   ├── os-core
+	#	  │   └── vim
+	#	  ├── swupd_lock
+	#	  └── version
+
+	# create the cache from "repo1"
+	create_third_party_repo -a "$TEST_NAME" 10 staging repo1
+	set_current_version "$TEST_NAME" 20 repo1
+
+	sudo mkdir -p "$TPSTATEDIR_MANIFEST"/{10,20}
+	MOM=$(create_manifest "$TPSTATEDIR_MANIFEST"/20 MoM 1 10)
+	write_to_protected_file -a "$MOM" "M...	dfd541b1ac9256982044848f2128f51e23ddbb72f68e9de43adaf8f7ead93657	10	p11-kit\n"
+	write_to_protected_file -a "$MOM" "M...	7414710480607fa89c307ad11d145d8bb0cbdbdf3c0692f940d906b670f6fd5d	20	emacs\n"
+	MOM_SIG="$MOM".sig ; sudo touch "$MOM_SIG"
+	FILE1="$TPSTATEDIR_MANIFEST"/10/Manifest.p11-kit ; sudo touch "$FILE1"
+	FILE2="$TPSTATEDIR_MANIFEST"/10/Manifest.p11-kit.dfd541b1ac9256982044848f2128f51e23ddbb72f68e9de43adaf8f7ead93657 ; sudo touch "$FILE2"
+	FILE3="$TPSTATEDIR_MANIFEST"/20/Manifest.emacs ; sudo touch "$FILE3"
+	FILE4="$TPSTATEDIR_MANIFEST"/20/Manifest.emacs.7414710480607fa89c307ad11d145d8bb0cbdbdf3c0692f940d906b670f6fd5d ; sudo touch "$FILE4"
+	FILE5="$TPSTATEDIR_MANIFEST"/Manifest-emacs-delta-from-10-to-20 ; sudo touch "$FILE5"
+	FILE6="$TPSTATEDIR_MANIFEST"/Manifest-vim-delta-from-10-to-20 ; sudo touch "$FILE6"
+	FILE7="$TPSTATEDIR_CACHE"/pack-blender-from-0-to-20.tar ; sudo touch "$FILE7"
+	FILE8="$TPSTATEDIR_CACHE"/pack-vim-from-10-to-20.tar ; sudo touch "$FILE8"
+	FILE9="$TPSTATEDIR_STAGED"/00004ead4b4eb1cef1ebbe13849f6c47c21d325182f98cf8f5333e9a76d2e2df ; sudo touch "$FILE9"
+	FILE10="$TPSTATEDIR_STAGED"/fffe891980af628e498b16a364b5b4d00377485370ccc4d09ac0fc072e85b31d ; sudo touch "$FILE10"
+
+	# create the cache from "repo2"
+	create_third_party_repo -a "$TEST_NAME" 10 staging repo2
+	set_current_version "$TEST_NAME" 50 repo2
+
+	sudo mkdir -p "$TPSTATEDIR_MANIFEST"/50
+	MOM2=$(create_manifest "$TPSTATEDIR_MANIFEST"/50 MoM 1 40)
+	write_to_protected_file -a "$MOM2" "M...	dfd541b1ac9256982044848f2128f51e23ddbb72f68e9de43adaf8f7ead12345	10	blender\n"
+	write_to_protected_file -a "$MOM2" "M...	1234510480607fa89c307ad11d145d8bb0cbdbdf3c0692f940d906b670f6fd5d	20	ansible\n"
+	MOM2_SIG="$MOM2".sig ; sudo touch "$MOM2_SIG"
+	FILE11="$TPSTATEDIR_MANIFEST"/Manifest-qt-basic-delta-from-40-to-50 ; sudo touch "$FILE11"
+	FILE12="$TPSTATEDIR_CACHE"/pack-lib-imageformat-from-30-to-50.tar ; sudo touch "$FILE12"
+	FILE13="$TPSTATEDIR_STAGED"/ffaf66dab58a2074e5fe9dc6ab7bf8773c069817dcccf631148b6afc87166b4b ; sudo touch "$FILE13"
+
+}
+
+@test "TPR098: Clean 3rd-party cached files except manifests" {
+
+	run sudo sh -c "$SWUPD 3rd-party clean $SWUPD_OPTS"
+
+	assert_status_is "$SWUPD_OK"
+	expected_output=$(cat <<-EOM
+		_____________________________
+		 3rd-Party Repository: repo1
+		_____________________________
+		12 files removed
+		.* KB freed
+		_____________________________
+		 3rd-Party Repository: repo2
+		_____________________________
+		7 files removed
+		.* KB freed
+	EOM
+	)
+	assert_regex_is_output "$expected_output"
+
+	# relevant manifests should still exist
+	assert_file_exists "$FILE1"
+	assert_file_exists "$FILE3"
+	assert_file_exists "$MOM"
+	assert_file_exists "$MOM_SIG"
+
+	# the rest of the files should not exist
+	assert_file_not_exists "$FILE2"
+	assert_file_not_exists "$FILE4"
+	assert_file_not_exists "$FILE5"
+	assert_file_not_exists "$FILE6"
+	assert_file_not_exists "$FILE7"
+	assert_file_not_exists "$FILE8"
+	assert_file_not_exists "$FILE9"
+	assert_file_not_exists "$FILE10"
+
+}
+
+@test "TPR099: Clean all 3rd-party cached files including manifests" {
+
+	run sudo sh -c "$SWUPD 3rd-party clean $SWUPD_OPTS --all"
+
+	assert_status_is "$SWUPD_OK"
+	expected_output=$(cat <<-EOM
+		_____________________________
+		 3rd-Party Repository: repo1
+		_____________________________
+		21 files removed
+		.* KB freed
+		_____________________________
+		 3rd-Party Repository: repo2
+		_____________________________
+		13 files removed
+		.* KB freed
+	EOM
+	)
+	assert_regex_is_output "$expected_output"
+
+	# everything should have been cleaned
+	assert_file_not_exists "$FILE1"
+	assert_file_not_exists "$FILE2"
+	assert_file_not_exists "$FILE3"
+	assert_file_not_exists "$FILE4"
+	assert_file_not_exists "$FILE5"
+	assert_file_not_exists "$FILE6"
+	assert_file_not_exists "$FILE7"
+	assert_file_not_exists "$FILE8"
+	assert_file_not_exists "$FILE9"
+	assert_file_not_exists "$FILE10"
+	assert_file_not_exists "$FILE11"
+	assert_file_not_exists "$FILE12"
+	assert_file_not_exists "$FILE13"
+	assert_file_not_exists "$MOM"
+	assert_file_not_exists "$MOM_SIG"
+	assert_file_not_exists "$MOM2"
+	assert_file_not_exists "$MOM2_SIG"
+
+}
+
+@test "TPR100: Dry run clean to show the 3rd-party files that would be removed from the cache" {
+
+	run sudo sh -c "$SWUPD 3rd-party clean $SWUPD_OPTS --dry-run"
+
+	assert_status_is "$SWUPD_OK"
+	expected_output=$(cat <<-EOM
+		_____________________________
+		 3rd-Party Repository: repo1
+		_____________________________
+		$STATEDIR_ABS/3rd-party/repo1/cache/.*repo1/pack-.*-from-.*-to-20.tar
+		$STATEDIR_ABS/3rd-party/repo1/cache/.*repo1/pack-.*-from-.*-to-20.tar
+		$STATEDIR_ABS/3rd-party/repo1/cache/.*repo1/delta
+		$STATEDIR_ABS/3rd-party/repo1/cache/.*repo1/download
+		$STATEDIR_ABS/3rd-party/repo1/cache/.*repo1/staged/.*
+		$STATEDIR_ABS/3rd-party/repo1/cache/.*repo1/staged/.*
+		$STATEDIR_ABS/3rd-party/repo1/cache/.*repo1/staged
+		$STATEDIR_ABS/3rd-party/repo1/cache/.*repo1/temp
+		$STATEDIR_ABS/3rd-party/repo1/cache/.*repo1/manifest/Manifest-.*-delta-from-10-to-20
+		$STATEDIR_ABS/3rd-party/repo1/cache/.*repo1/manifest/Manifest-.*-delta-from-10-to-20
+		$STATEDIR_ABS/3rd-party/repo1/cache/.*repo1/manifest/.0/Manifest\\..*\\..*
+		$STATEDIR_ABS/3rd-party/repo1/cache/.*repo1/manifest/.0/Manifest\\..*\\..*
+		Would remove 12 files
+		Aproximatelly .* KB would be freed
+		_____________________________
+		 3rd-Party Repository: repo2
+		_____________________________
+		$STATEDIR_ABS/3rd-party/repo2/cache/.*repo2/pack-lib-imageformat-from-30-to-50.tar
+		$STATEDIR_ABS/3rd-party/repo2/cache/.*repo2/delta
+		$STATEDIR_ABS/3rd-party/repo2/cache/.*repo2/download
+		$STATEDIR_ABS/3rd-party/repo2/cache/.*repo2/staged/ffaf66dab58a2074e5fe9dc6ab7bf8773c069817dcccf631148b6afc87166b4b
+		$STATEDIR_ABS/3rd-party/repo2/cache/.*repo2/staged
+		$STATEDIR_ABS/3rd-party/repo2/cache/.*repo2/temp
+		$STATEDIR_ABS/3rd-party/repo2/cache/.*repo2/manifest/Manifest-qt-basic-delta-from-40-to-50
+		Would remove 7 files
+		Aproximatelly .* KB would be freed
+	EOM
+	)
+	assert_regex_in_output "$expected_output"
+
+	# files should not be deleted, just printed
+	assert_file_exists "$FILE1"
+	assert_file_exists "$FILE2"
+	assert_file_exists "$FILE3"
+	assert_file_exists "$FILE4"
+	assert_file_exists "$FILE5"
+	assert_file_exists "$FILE6"
+	assert_file_exists "$FILE7"
+	assert_file_exists "$FILE8"
+	assert_file_exists "$FILE9"
+	assert_file_exists "$FILE10"
+	assert_file_exists "$FILE11"
+	assert_file_exists "$FILE12"
+	assert_file_exists "$FILE13"
+	assert_file_exists "$MOM"
+	assert_file_exists "$MOM_SIG"
+	assert_file_exists "$MOM"
+	assert_file_exists "$MOM_SIG"
+	assert_file_exists "$MOM2"
+	assert_file_exists "$MOM2_SIG"
+
+}
diff --git a/test/functional/api/api-3rd-party-clean.bats b/test/functional/api/api-3rd-party-clean.bats
index ca7f832c..957ec0c0 100755
--- a/test/functional/api/api-3rd-party-clean.bats
+++ b/test/functional/api/api-3rd-party-clean.bats
@@ -8,14 +8,16 @@ load "../testlib"
 test_setup() {
 
 	create_test_environment "$TEST_NAME" 10 1
+
 	create_third_party_repo -a "$TEST_NAME" 10 1 repo1
-	STATE1="$TPSTATEDIR"
-	sudo mkdir -p "$STATE1"/manifest/10
-	sudo touch "$STATE1"/manifest/10/Manifest.test{1..3}
-	sudo touch "$STATE1"/pack-test{1..2}-from-0.tar
+	CACHE1="$TPSTATEDIR_CACHE"
+	sudo mkdir -p "$TPSTATEDIR_MANIFEST"/10
+	sudo touch "$TPSTATEDIR_MANIFEST"/10/Manifest.test{1..3}
+	sudo touch "$CACHE1"/pack-test{1..2}-from-0.tar
+
 	create_third_party_repo -a "$TEST_NAME" 10 1 repo2
-	STATE2="$TPSTATEDIR"
-	sudo touch "$STATE2"/pack-test3-from-0.tar
+	CACHE2="$TPSTATEDIR_CACHE"
+	sudo touch "$CACHE2"/pack-test3-from-0.tar
 
 }
 
@@ -41,13 +43,21 @@ test_setup() {
 	assert_status_is "$SWUPD_OK"
 	expected_output=$(cat <<-EOM
 		\\[repo1\\]
-		$TEST_ROOT_DIR/$STATE1/pack-test.-from-0.tar
-		$TEST_ROOT_DIR/$STATE1/pack-test.-from-0.tar
-		$TEST_ROOT_DIR/$STATE1/manifest/10/Manifest.test.
-		$TEST_ROOT_DIR/$STATE1/manifest/10/Manifest.test.
-		$TEST_ROOT_DIR/$STATE1/manifest/10/Manifest.test.
+		$CACHE1/pack-test.-from-0.tar
+		$CACHE1/pack-test.-from-0.tar
+		$CACHE1/delta
+		$CACHE1/download
+		$CACHE1/staged
+		$CACHE1/temp
+		$CACHE1/manifest/10/Manifest.test.
+		$CACHE1/manifest/10/Manifest.test.
+		$CACHE1/manifest/10/Manifest.test.
 		\\[repo2\\]
-		$TEST_ROOT_DIR/$STATE2/pack-test3-from-0.tar
+		$CACHE2/pack-test3-from-0.tar
+		$CACHE2/delta
+		$CACHE2/download
+		$CACHE2/staged
+		$CACHE2/temp
 	EOM
 	)
 	assert_regex_is_output "$expected_output"
@@ -60,11 +70,15 @@ test_setup() {
 
 	assert_status_is "$SWUPD_OK"
 	expected_output=$(cat <<-EOM
-		$TEST_ROOT_DIR/$STATE1/pack-test.-from-0.tar
-		$TEST_ROOT_DIR/$STATE1/pack-test.-from-0.tar
-		$TEST_ROOT_DIR/$STATE1/manifest/10/Manifest.test.
-		$TEST_ROOT_DIR/$STATE1/manifest/10/Manifest.test.
-		$TEST_ROOT_DIR/$STATE1/manifest/10/Manifest.test.
+		$CACHE1/pack-test.-from-0.tar
+		$CACHE1/pack-test.-from-0.tar
+		$CACHE1/delta
+		$CACHE1/download
+		$CACHE1/staged
+		$CACHE1/temp
+		$CACHE1/manifest/10/Manifest.test.
+		$CACHE1/manifest/10/Manifest.test.
+		$CACHE1/manifest/10/Manifest.test.
 	EOM
 	)
 	assert_regex_is_output "$expected_output"
diff --git a/test/functional/api/api-clean.bats b/test/functional/api/api-clean.bats
index aacd8c67..b25decc3 100755
--- a/test/functional/api/api-clean.bats
+++ b/test/functional/api/api-clean.bats
@@ -8,9 +8,9 @@ load "../testlib"
 test_setup() {
 
 	create_test_environment "$TEST_NAME"
-	sudo mkdir "$STATEDIR"/manifest/10
-	sudo touch "$STATEDIR"/manifest/10/Manifest.test{1..3}
-	sudo touch "$STATEDIR"/pack-test{1..2}-from-0.tar
+	sudo mkdir "$STATEDIR_MANIFEST"/10
+	sudo touch "$STATEDIR_MANIFEST"/10/Manifest.test{1..3}
+	sudo touch "$STATEDIR_CACHE"/pack-test{1..2}-from-0.tar
 
 }
 
@@ -29,11 +29,15 @@ test_setup() {
 
 	assert_status_is "$SWUPD_OK"
 	expected_output=$(cat <<-EOM
-		$TEST_ROOT_DIR/$STATEDIR/pack-test.-from-0.tar
-		$TEST_ROOT_DIR/$STATEDIR/pack-test.-from-0.tar
-		$TEST_ROOT_DIR/$STATEDIR/manifest/10/Manifest.test.
-		$TEST_ROOT_DIR/$STATEDIR/manifest/10/Manifest.test.
-		$TEST_ROOT_DIR/$STATEDIR/manifest/10/Manifest.test.
+		$STATEDIR_CACHE/pack-test.-from-0.tar
+		$STATEDIR_CACHE/pack-test.-from-0.tar
+		$STATEDIR_DELTA
+		$STATEDIR_DOWNLOAD
+		$STATEDIR_STAGED
+		$STATEDIR_TEMP
+		$STATEDIR_MANIFEST/10/Manifest.test.
+		$STATEDIR_MANIFEST/10/Manifest.test.
+		$STATEDIR_MANIFEST/10/Manifest.test.
 	EOM
 	)
 	assert_regex_is_output "$expected_output"
diff --git a/test/functional/clean/clean-basic.bats b/test/functional/clean/clean-basic.bats
new file mode 100755
index 00000000..58481ce8
--- /dev/null
+++ b/test/functional/clean/clean-basic.bats
@@ -0,0 +1,174 @@
+#!/usr/bin/env bats
+
+# Author: Castulo Martinez
+# Email: castulo.martinez@intel.com
+
+load "../testlib"
+
+test_setup() {
+
+	create_test_environment "$TEST_NAME"
+	set_current_version "$TEST_NAME" 33000
+
+	# ########################################################
+	# cache/data structure post swupd 4.2.1 (split cache/data)
+	# ########################################################
+	# <cachedir>
+	# └── cache
+	#     ├── https_cdn.download.clearlinux.org_update
+	#     │   ├── delta
+	#     │   ├── download
+	#     │   ├── manifest
+	#     │   │   ├── 32900
+	#     │   │   │   ├── Manifest.p11-kit
+	#     │   │   │   └── Manifest.p11-kit.dfd541b1ac9256982044848f2128f51e23ddbb72f68e9de43adaf8f7ead93657
+	#     │   │   ├── 33000
+	#     │   │   │   ├── Manifest.MoM
+	#     │   │   │   ├── Manifest.MoM.sig
+	#     │   │   │   ├── Manifest.emacs
+	#     │   │   │   └── Manifest.emacs.7414710480607fa89c307ad11d145d8bb0cbdbdf3c0692f940d906b670f6fd5d
+	#     │   │   ├── Manifest-emacs-delta-from-32900-to-33000
+	#     │   │   └── Manifest-vim-delta-from-32900-to-33000
+	#     │   ├── pack-blender-from-0-to-33000.tar
+	#     │   ├── pack-vim-from-32800-to-32900.tar
+	#     │   ├── staged
+	#     │   │   ├── 00004ead4b4eb1cef1ebbe13849f6c47c21d325182f98cf8f5333e9a76d2e2df
+	#     │   │   └── fffe891980af628e498b16a364b5b4d00377485370ccc4d09ac0fc072e85b31d
+	#     │   └── temp
+	#     └── https_other.clearlinux.update_site
+	#         ├── delta
+	#         ├── download
+	#         ├── manifest
+	#         │   ├── 32900
+	#         │   │   ├── Manifest.MoM
+	#         │   │   └── Manifest.MoM.sig
+	#         │   └── Manifest-qt-basic-delta-from-33010-to-33140
+	#         ├── pack-lib-imageformat-from-33090-to-33170.tar
+	#         ├── staged
+	#         │   └── ffaf66dab58a2074e5fe9dc6ab7bf8773c069817dcccf631148b6afc87166b4b
+	#         └── temp
+
+	# <datadir>
+	# │
+	# ├── bundles
+	# │   ├── editors
+	# │   ├── os-core
+	# │   └── vim
+	# ├── telemetry
+	# │   ├── 2.packmissing.1.Zh11gI
+	# │   └── 2.verify.1.4hR0jx
+	# ├── swupd_lock
+	# └── version
+
+	sudo mkdir -p "$STATEDIR_CACHE"/{delta,download,manifest,staged}
+	sudo chmod 0700 "$STATEDIR_CACHE"/staged
+	sudo mkdir -p "$STATEDIR_MANIFEST"/{32900,33000}
+
+	MOM=$(create_manifest "$STATEDIR_MANIFEST"/33000 MoM 1 32900)
+	write_to_protected_file -a "$MOM" "M...	dfd541b1ac9256982044848f2128f51e23ddbb72f68e9de43adaf8f7ead93657	32900	p11-kit\n"
+	write_to_protected_file -a "$MOM" "M...	7414710480607fa89c307ad11d145d8bb0cbdbdf3c0692f940d906b670f6fd5d	33000	emacs\n"
+	MOM_SIG="$MOM".sig ; sudo touch "$MOM_SIG"
+
+	FILE1="$STATEDIR_MANIFEST"/32900/Manifest.p11-kit ; sudo touch "$FILE1"
+	FILE2="$STATEDIR_MANIFEST"/32900/Manifest.p11-kit.dfd541b1ac9256982044848f2128f51e23ddbb72f68e9de43adaf8f7ead93657 ; sudo touch "$FILE2"
+	FILE3="$STATEDIR_MANIFEST"/33000/Manifest.emacs ; sudo touch "$FILE3"
+	FILE4="$STATEDIR_MANIFEST"/33000/Manifest.emacs.7414710480607fa89c307ad11d145d8bb0cbdbdf3c0692f940d906b670f6fd5d ; sudo touch "$FILE4"
+	FILE5="$STATEDIR_MANIFEST"/Manifest-emacs-delta-from-32900-to-33000 ; sudo touch "$FILE5"
+	FILE6="$STATEDIR_MANIFEST"/Manifest-vim-delta-from-32900-to-33000 ; sudo touch "$FILE6"
+	FILE7="$STATEDIR_CACHE"/pack-blender-from-0-to-33000.tar ; sudo touch "$FILE7"
+	FILE8="$STATEDIR_CACHE"/pack-vim-from-32800-to-32900.tar ; sudo touch "$FILE8"
+	FILE9="$STATEDIR_STAGED"/00004ead4b4eb1cef1ebbe13849f6c47c21d325182f98cf8f5333e9a76d2e2df ; sudo touch "$FILE9"
+	FILE10="$STATEDIR_STAGED"/fffe891980af628e498b16a364b5b4d00377485370ccc4d09ac0fc072e85b31d ; sudo touch "$FILE10"
+	# second url cache
+	sudo mkdir -p "$STATEDIR_ABS"/cache/https_other.clearlinux.update_site/{delta,download,manifest,staged,temp}
+	sudo mkdir -p "$STATEDIR_ABS"/cache/https_other.clearlinux.update_site/manifest/32900
+	FILE11="$STATEDIR_ABS"/cache/https_other.clearlinux.update_site/pack-lib-imageformat-from-33090-to-33170.tar ; sudo touch "$FILE11"
+	FILE12="$STATEDIR_ABS"/cache/https_other.clearlinux.update_site/manifest/32900/Manifest.MoM ; sudo touch "$FILE12"
+	FILE13="$STATEDIR_ABS"/cache/https_other.clearlinux.update_site/manifest/32900/Manifest.MoM.sig ; sudo touch "$FILE13"
+	FILE14="$STATEDIR_ABS"/cache/https_other.clearlinux.update_site/manifest/Manifest-qt-basic-delta-from-33010-to-33140 ; sudo touch "$FILE14"
+	FILE15="$STATEDIR_ABS"/cache/https_other.clearlinux.update_site/staged/ffaf66dab58a2074e5fe9dc6ab7bf8773c069817dcccf631148b6afc87166b4b ; sudo touch "$FILE15"
+
+}
+
+@test "CLN001: Clean cached files except manifests" {
+
+	run sudo sh -c "$SWUPD clean $SWUPD_OPTS"
+
+	assert_status_is "$SWUPD_OK"
+	expected_output=$(cat <<-EOM
+		24 files removed
+		.* KB freed
+	EOM
+	)
+	assert_regex_is_output "$expected_output"
+
+	# relevant manifests should still exist
+	assert_file_exists "$STATEDIR_MANIFEST"/32900/Manifest.p11-kit
+	assert_file_exists "$STATEDIR_MANIFEST"/33000/Manifest.emacs
+	assert_file_exists "$STATEDIR_MANIFEST"/33000/Manifest.MoM
+	assert_file_exists "$STATEDIR_MANIFEST"/33000/Manifest.MoM.sig
+
+	# the rest of the files should not exist
+	assert_file_not_exists "$FILE2"
+	assert_file_not_exists "$FILE4"
+	assert_file_not_exists "$FILE5"
+	assert_file_not_exists "$FILE6"
+	assert_file_not_exists "$FILE7"
+	assert_file_not_exists "$FILE8"
+	assert_dir_not_exists "$STATEDIR_STAGED"
+	assert_dir_not_exists "$STATEDIR_DOWNLOAD"
+	assert_dir_not_exists "$STATEDIR_DELTA"
+	assert_dir_not_exists "$STATEDIR_ABS"/cache/https_other.clearlinux.update_site
+
+}
+
+@test "CLN002: Clean all cached files including manifests" {
+
+	run sudo sh -c "$SWUPD clean $SWUPD_OPTS --all"
+
+	assert_status_is "$SWUPD_OK"
+	expected_output=$(cat <<-EOM
+		33 files removed
+		.* KB freed
+	EOM
+	)
+	assert_regex_is_output "$expected_output"
+
+	# everything should have been cleaned
+	assert_dir_not_exists "$STATEDIR_ABS"/cache
+
+}
+
+@test "CLN003: Dry run clean to show the files that would be removed from the cache" {
+
+	run sudo sh -c "$SWUPD clean $SWUPD_OPTS --dry-run"
+
+	assert_status_is "$SWUPD_OK"
+	expected_output=$(cat <<-EOM
+		$STATEDIR_ABS/cache/https_other.clearlinux.update_site
+		Would remove 24 files
+		Aproximatelly .* KB would be freed
+	EOM
+	)
+	assert_regex_in_output "$expected_output"
+
+	# files should not be deleted, just printed
+	assert_file_exists "$FILE1"
+	assert_file_exists "$FILE2"
+	assert_file_exists "$FILE3"
+	assert_file_exists "$FILE4"
+	assert_file_exists "$FILE5"
+	assert_file_exists "$FILE6"
+	assert_file_exists "$FILE7"
+	assert_file_exists "$FILE8"
+	assert_file_exists "$FILE9"
+	assert_file_exists "$FILE10"
+	assert_file_exists "$FILE11"
+	assert_file_exists "$FILE12"
+	assert_file_exists "$FILE13"
+	assert_file_exists "$FILE14"
+	assert_file_exists "$FILE15"
+	assert_file_exists "$MOM"
+	assert_file_exists "$MOM_SIG"
+
+}
diff --git a/test/functional/clean/clean-grouped-manifests.bats b/test/functional/clean/clean-grouped-manifests.bats
new file mode 100755
index 00000000..18eff501
--- /dev/null
+++ b/test/functional/clean/clean-grouped-manifests.bats
@@ -0,0 +1,152 @@
+#!/usr/bin/env bats
+
+# Author: Castulo Martinez
+# Email: castulo.martinez@intel.com
+
+load "../testlib"
+
+test_setup() {
+
+	create_test_environment "$TEST_NAME"
+	set_current_version "$TEST_NAME" 33000
+
+	# #################################################
+	# statedir structure 4.2.1 (with grouped manifests)
+	# #################################################
+	# <statedir>
+	# ├── manifest
+	# │   ├── 32900
+	# │   │   ├── Manifest.editors
+	# │   │   └── Manifest.editors.8f7aca1643c1cd8b109774b65c83c0dad5a2d259348343a9395fd63f71640c63
+	# │   ├── 33000
+	# │   │   ├── Manifest.MoM
+	# │   │   ├── Manifest.MoM.sig
+	# │   │   ├── Manifest.emacs
+	# │   │   └── Manifest.emacs.7414710480607fa89c307ad11d145d8bb0cbdbdf3c0692f940d906b670f6fd5d
+	# │   └── Manifest-emacs-delta-from-32900-to-33000
+	# ├── delta
+	# ├── download
+	# ├── pack-vim-from-32800-to-32900.tar
+	# ├── staged
+	# │   ├── 00004ead4b4eb1cef1ebbe13849f6c47c21d325182f98cf8f5333e9a76d2e2df
+	# │   └── fffe891980af628e498b16a364b5b4d00377485370ccc4d09ac0fc072e85b31d
+	# │
+
+	# 3rd-party has both, data and cache
+
+    # │
+	# ├── 3rd-party
+	# │
+
+	# From here on it is just data
+
+	# │
+	# ├── bundles
+	# │   ├── editors
+	# │   ├── emacs
+	# │   ├── os-core
+	# │   └── vim
+	# ├── telemetry
+	# │   ├── 2.update.1.Dpjz7G
+	# │   └── 2.verify.1.4hR0jx
+	# ├── swupd_lock
+	# └── version
+
+	sudo mkdir -p "$STATEDIR_ABS"/manifest/{32900,33000}
+	sudo mkdir -p "$STATEDIR_ABS"/{staged,delta,download}
+
+	MOM="$STATEDIR_ABS"/manifest/33000/Manifest.MoM ; sudo touch "$MOM"
+	MOM_SIG="$STATEDIR_ABS"/manifest/33000/Manifest.MoM.sig ; sudo touch "$MOM_SIG"
+	FILE1="$STATEDIR_ABS"/manifest/32900/Manifest.editors ; sudo touch "$FILE1"
+	FILE2="$STATEDIR_ABS"/manifest/32900/Manifest.editors.8f7aca1643c1cd8b109774b65c83c0dad5a2d259348343a9395fd63f71640c63 ; sudo touch "$FILE2"
+	FILE3="$STATEDIR_ABS"/manifest/33000/Manifest.emacs ; sudo touch "$FILE3"
+	FILE4="$STATEDIR_ABS"/manifest/33000/Manifest.emacs.7414710480607fa89c307ad11d145d8bb0cbdbdf3c0692f940d906b670f6fd5d ; sudo touch "$FILE4"
+	FILE5="$STATEDIR_ABS"/manifest/Manifest-emacs-delta-from-32900-to-33000 ; sudo touch "$FILE5"
+	FILE6="$STATEDIR_ABS"/pack-vim-from-32800-to-32900.tar ; sudo touch "$FILE6"
+	FILE7="$STATEDIR_ABS"/staged/00004ead4b4eb1cef1ebbe13849f6c47c21d325182f98cf8f5333e9a76d2e2df ; sudo touch "$FILE7"
+	FILE8="$STATEDIR_ABS"/staged/fffe891980af628e498b16a364b5b4d00377485370ccc4d09ac0fc072e85b31d ; sudo touch "$FILE8"
+
+	sudo chmod -R 0700 "$STATEDIR_ABS"
+
+}
+
+@test "CLN006: Clean cached files in the 4.2.1 statedir structure" {
+
+	# during release 4.2.1 swupd used a statedir that contained both, cache
+	# and data, but all manifest related artifcts were grouped within the
+	# "manifest" directory. We need to make sure we are still cleaning those
+	# files regardless of if the user used the --all flag or not since that
+	# cache is not going to be used anymore anyway.
+
+	run sudo sh -c "$SWUPD clean $SWUPD_OPTS"
+
+	assert_status_is "$SWUPD_OK"
+	expected_output=$(cat <<-EOM
+		20 files removed
+		.* KB freed
+	EOM
+	)
+	assert_regex_is_output "$expected_output"
+
+	# these old directories should be removed since are no longer used
+	assert_dir_not_exists "$STATEDIR_ABS"/delta
+	assert_dir_not_exists "$STATEDIR_ABS"/download
+	assert_dir_not_exists "$STATEDIR_ABS"/staged
+	assert_dir_not_exists "$STATEDIR_ABS"/manifest
+
+	# files in the old structure should no longer be there either
+	assert_file_not_exists "$STATEDIR_ABS"/Manifest-emacs-delta-from-32900-to-33000
+	assert_file_not_exists "$STATEDIR_ABS"/pack-vim-from-32800-to-32900.tar
+
+}
+
+@test "CLN007: Dry run includes files in the 4.2.1 statedir structure" {
+
+	# during release 4.2.1 swupd used a statedir that contained both, cache
+	# and data, but all manifest related artifcts were grouped within the
+	# "manifest" directory. If the user runs a "clean --dry-run" we should
+	# include those files in the list of things that will be removed.
+
+	run sudo sh -c "$SWUPD clean $SWUPD_OPTS --dry-run"
+
+	assert_status_is "$SWUPD_OK"
+	expected_output=$(cat <<-EOM
+		$STATEDIR_DELTA
+		$STATEDIR_DOWNLOAD
+		$STATEDIR_STAGED
+		$STATEDIR_TEMP
+		$STATEDIR_ABS/pack-vim-from-32800-to-32900.tar
+		$STATEDIR_ABS/staged/.*
+		$STATEDIR_ABS/staged/.*
+		$STATEDIR_ABS/staged
+		$STATEDIR_ABS/manifest/Manifest-emacs-delta-from-32900-to-33000
+		$STATEDIR_ABS/manifest/32900/Manifest\\..*
+		$STATEDIR_ABS/manifest/32900/Manifest\\..*
+		$STATEDIR_ABS/manifest/32900
+		$STATEDIR_ABS/manifest/33000/Manifest\\..*
+		$STATEDIR_ABS/manifest/33000/Manifest\\..*
+		$STATEDIR_ABS/manifest/33000/Manifest\\..*
+		$STATEDIR_ABS/manifest/33000/Manifest\\..*
+		$STATEDIR_ABS/manifest/33000
+		$STATEDIR_ABS/manifest
+		$STATEDIR_ABS/delta
+		$STATEDIR_ABS/download
+		Would remove 20 files
+		Aproximatelly .* KB would be freed
+	EOM
+	)
+	assert_regex_is_output "$expected_output"
+
+	# non of the files should be removed since it was just a dry run
+	assert_file_exists "$MOM"
+	assert_file_exists "$MOM_SIG"
+	assert_file_exists "$FILE1"
+	assert_file_exists "$FILE2"
+	assert_file_exists "$FILE3"
+	assert_file_exists "$FILE4"
+	assert_file_exists "$FILE5"
+	assert_file_exists "$FILE6"
+	assert_file_exists "$FILE7"
+	assert_file_exists "$FILE8"
+
+}
diff --git a/test/functional/clean/clean-old-statedir.bats b/test/functional/clean/clean-old-statedir.bats
new file mode 100755
index 00000000..112094bb
--- /dev/null
+++ b/test/functional/clean/clean-old-statedir.bats
@@ -0,0 +1,147 @@
+#!/usr/bin/env bats
+
+# Author: Castulo Martinez
+# Email: castulo.martinez@intel.com
+
+load "../testlib"
+
+test_setup() {
+
+	create_test_environment "$TEST_NAME"
+	set_current_version "$TEST_NAME" 33000
+
+	# ###########################
+	# statedir structure <= 4.2.0
+	# ###########################
+	# <statedir>
+	# ├── 32900
+	# │   ├── Manifest.p11-kit
+	# │   └── Manifest.p11-kit.dfd541b1ac9256982044848f2128f51e23ddbb72f68e9de43adaf8f7ead93657
+	# ├── 33000
+	# │   ├── Manifest.MoM
+	# │   ├── Manifest.MoM.sig
+	# │   ├── Manifest.emacs
+	# │   └── Manifest.emacs.7414710480607fa89c307ad11d145d8bb0cbdbdf3c0692f940d906b670f6fd5d
+	# ├── delta
+	# ├── download
+	# ├── Manifest-emacs-delta-from-32900-to-33000
+	# ├── pack-vim-from-32800-to-32900.tar
+	# ├── staged
+	# │   ├── 00004ead4b4eb1cef1ebbe13849f6c47c21d325182f98cf8f5333e9a76d2e2df
+	# │   └── fffe891980af628e498b16a364b5b4d00377485370ccc4d09ac0fc072e85b31d
+
+	# 3rd-party has both, data and cache
+
+    # │
+	# ├── 3rd-party
+	# │
+
+	# From here on it is just data
+
+	# │
+	# ├── bundles
+	# │   ├── editors
+	# │   ├── os-core
+	# │   └── vim
+	# ├── telemetry
+	# │   ├── 2.packmissing.1.Zh11gI
+	# │   └── 2.verify.1.4hR0jx
+	# ├── swupd_lock
+	# └── version
+
+	sudo mkdir -p "$STATEDIR_ABS"/{32900,33000,delta,download,staged}
+
+	MOM="$STATEDIR_ABS"/33000/Manifest.MoM ; sudo touch "$MOM"
+	MOM_SIG="$STATEDIR_ABS"/33000/Manifest.MoM.sig ; sudo touch "$MOM_SIG"
+	FILE1="$STATEDIR_ABS"/32900/Manifest.p11-kit ; sudo touch "$FILE1"
+	FILE2="$STATEDIR_ABS"/32900/Manifest.p11-kit.dfd541b1ac9256982044848f2128f51e23ddbb72f68e9de43adaf8f7ead93657 ; sudo touch "$FILE2"
+	FILE3="$STATEDIR_ABS"/33000/Manifest.emacs ; sudo touch "$FILE3"
+	FILE4="$STATEDIR_ABS"/33000/Manifest.emacs.7414710480607fa89c307ad11d145d8bb0cbdbdf3c0692f940d906b670f6fd5d ; sudo touch "$FILE4"
+	FILE5="$STATEDIR_ABS"/Manifest-emacs-delta-from-32900-to-33000 ; sudo touch "$FILE5"
+	FILE6="$STATEDIR_ABS"/pack-vim-from-32800-to-32900.tar ; sudo touch "$FILE6"
+	FILE7="$STATEDIR_ABS"/staged/00004ead4b4eb1cef1ebbe13849f6c47c21d325182f98cf8f5333e9a76d2e2df ; sudo touch "$FILE7"
+	FILE8="$STATEDIR_ABS"/staged/fffe891980af628e498b16a364b5b4d00377485370ccc4d09ac0fc072e85b31d ; sudo touch "$FILE8"
+
+	sudo chmod -R 0700 "$STATEDIR_ABS"
+
+}
+
+@test "CLN004: Clean cached files in the pre 4.2.1 statedir structure" {
+
+	# before release 4.2.0 swupd used a statedir that contained both, cache
+	# and data. We need to make sure we are still cleaning that in case users
+	# have the old statedir structure still in their system. We should clean
+	# everything in the old structure regardless of if the user used the
+	# --all flag or not since that cache is not going to be used anymore anyway.
+
+	run sudo sh -c "$SWUPD clean $SWUPD_OPTS"
+
+	assert_status_is "$SWUPD_OK"
+	expected_output=$(cat <<-EOM
+		19 files removed
+		.* KB freed
+	EOM
+	)
+	assert_regex_is_output "$expected_output"
+
+	# these old directories should be removed since are no longer used
+	assert_dir_not_exists "$STATEDIR_ABS"/delta
+	assert_dir_not_exists "$STATEDIR_ABS"/download
+	assert_dir_not_exists "$STATEDIR_ABS"/staged
+	assert_dir_not_exists "$STATEDIR_ABS"/32900
+	assert_dir_not_exists "$STATEDIR_ABS"/33000
+
+	# files in the old structure should no longer be there either
+	assert_file_not_exists "$STATEDIR_ABS"/Manifest-emacs-delta-from-32900-to-33000
+	assert_file_not_exists "$STATEDIR_ABS"/pack-vim-from-32800-to-32900.tar
+
+}
+
+@test "CLN005: Dry run includes files in the pre 4.2.1 statedir structure" {
+
+	# before release 4.2.0 swupd used a statedir that contained both, cache
+	# and data. If the user runs a "clean --dry-run" we should include those
+	# files in the list of things that will be removed.
+
+	run sudo sh -c "$SWUPD clean $SWUPD_OPTS --dry-run"
+
+	assert_status_is "$SWUPD_OK"
+	expected_output=$(cat <<-EOM
+		$STATEDIR_DELTA
+		$STATEDIR_DOWNLOAD
+		$STATEDIR_STAGED
+		$STATEDIR_TEMP
+		$STATEDIR_ABS/pack-vim-from-32800-to-32900.tar
+		$STATEDIR_ABS/Manifest-emacs-delta-from-32900-to-33000
+		$STATEDIR_ABS/staged/.*
+		$STATEDIR_ABS/staged/.*
+		$STATEDIR_ABS/staged
+		$STATEDIR_ABS/delta
+		$STATEDIR_ABS/download
+		$STATEDIR_ABS/32900/Manifest\\..*
+		$STATEDIR_ABS/32900/Manifest\\..*
+		$STATEDIR_ABS/32900
+		$STATEDIR_ABS/33000/Manifest\\..*
+		$STATEDIR_ABS/33000/Manifest\\..*
+		$STATEDIR_ABS/33000/Manifest\\..*
+		$STATEDIR_ABS/33000/Manifest\\..*
+		$STATEDIR_ABS/33000
+		Would remove 19 files
+		Aproximatelly .* KB would be freed
+	EOM
+	)
+	assert_regex_is_output "$expected_output"
+
+	# non of the files should be removed since it was just a dry run
+	assert_file_exists "$MOM"
+	assert_file_exists "$MOM_SIG"
+	assert_file_exists "$FILE1"
+	assert_file_exists "$FILE2"
+	assert_file_exists "$FILE3"
+	assert_file_exists "$FILE4"
+	assert_file_exists "$FILE5"
+	assert_file_exists "$FILE6"
+	assert_file_exists "$FILE7"
+	assert_file_exists "$FILE8"
+
+}
diff --git a/test/functional/signature/permission-incorrect.bats b/test/functional/signature/permission-incorrect.bats
index 28795233..dbedf1cb 100755
--- a/test/functional/signature/permission-incorrect.bats
+++ b/test/functional/signature/permission-incorrect.bats
@@ -71,6 +71,11 @@ test_setup() {
 	assert_status_is 0
 	assert_in_output "700"
 
+	# staged directory should only be accesible by root
+	run sudo sh -c "stat -c '%a' $STATEDIR_STAGED"
+	assert_status_is 0
+	assert_in_output "700"
+
 }
 
 @test "SIG028: Check if state dir permissions are correct after execution even if they are wrong before" {