diff --git a/src/manifest.c b/src/manifest.c
index dbbedaac..da23fba9 100644
--- a/src/manifest.c
+++ b/src/manifest.c
@@ -1108,19 +1108,22 @@ void remove_files_in_manifest_from_fs(struct manifest *m)
 	struct list *iter = NULL;
 	struct file *file = NULL;
 	char *fullfile = NULL;
-	int count = 0;
+	int count = list_len(m->files);
 
 	iter = list_head(m->files);
 	while (iter) {
 		file = iter->data;
 		iter = iter->next;
 		string_or_die(&fullfile, "%s/%s", path_prefix, file->filename);
-		if (swupd_rm(fullfile) != 0) {
-			free_string(&fullfile);
-			continue;
+		if (swupd_rm(fullfile) == -1) {
+			/* if a -1 is returned it means there was an issue deleting the
+			 * file or directory, in that case decrease the counter of deleted
+			 * files.
+			 * Note: If a file didn't exist it will still be counted as deleted,
+			 * this is a limitation */
+			count--;
 		}
 		free_string(&fullfile);
-		count++;
 	}
 	fprintf(stderr, "Total deleted files: %i\n", count);
 }
diff --git a/test/functional/bundleremove/remove-basics.bats b/test/functional/bundleremove/remove-basics.bats
index 9090ae2d..fa9f254d 100755
--- a/test/functional/bundleremove/remove-basics.bats
+++ b/test/functional/bundleremove/remove-basics.bats
@@ -5,8 +5,8 @@ load "../testlib"
 global_setup() {
 
 	create_test_environment "$TEST_NAME"
-	create_bundle -L -n test-bundle1 -d /foo -f /test-file1,/bar/test-file2,/bat/test-file3 "$TEST_NAME"
-	create_bundle -L -n test-bundle2 -f /bat/test-file4 "$TEST_NAME"
+	create_bundle -L -n test-bundle1 -d /foo -f /test-file1,/bar/test-file2,/bat/test-file3,/bat/common "$TEST_NAME"
+	create_bundle -L -n test-bundle2 -f /bat/test-file4,/bat/common "$TEST_NAME"
 	create_bundle -n test-bundle3 -f /baz/test-file5 "$TEST_NAME"
 
 }
@@ -51,14 +51,14 @@ global_teardown() {
 	# bundle2 was not removed
 	assert_file_exists "$TARGETDIR"/usr/share/clear/bundles/test-bundle2
 	assert_file_exists "$TARGETDIR"/bat/test-file4
+	assert_file_exists "$TARGETDIR"/bat/common
 	expected_output=$(cat <<-EOM
 		Deleting bundle files...
-		Total deleted files: 5
+		Total deleted files: 6
 		Successfully removed 1 bundle
 	EOM
 	)
 	assert_is_output --identical "$expected_output"
-	# TODO(castulo): The total deleted files should have been 6, change once bug #690 is fixed
 
 }
 
@@ -73,21 +73,22 @@ global_teardown() {
 	assert_file_not_exists "$TARGETDIR"/test-file1
 	assert_file_not_exists "$TARGETDIR"/bar/test-file2
 	assert_file_not_exists "$TARGETDIR"/bat/test-file3
+	assert_file_not_exists "$TARGETDIR"/bat/test-file4
+	assert_file_not_exists "$TARGETDIR"/bat/common
 	assert_dir_not_exists "$TARGETDIR"/foo
 	assert_dir_not_exists "$TARGETDIR"/bar
 	assert_dir_not_exists "$TARGETDIR"/bat
 	expected_output=$(cat <<-EOM
 		Removing bundle: test-bundle1
 		Deleting bundle files...
-		Total deleted files: 5
+		Total deleted files: 6
 		Removing bundle: test-bundle2
 		Deleting bundle files...
-		Total deleted files: 2
+		Total deleted files: 4
 		Successfully removed 2 bundles
 	EOM
 	)
 	assert_is_output --identical "$expected_output"
-	# TODO(castulo): The total deleted files should have been 7 + 2, change once bug #690 is fixed
 
 }
 
@@ -156,16 +157,16 @@ global_teardown() {
 	# bundle2 was not removed
 	assert_file_exists "$TARGETDIR"/usr/share/clear/bundles/test-bundle2
 	assert_file_exists "$TARGETDIR"/bat/test-file4
+	assert_file_exists "$TARGETDIR"/bat/common
 	expected_output=$(cat <<-EOM
 		Warning: Bundle "test-bundle3" is not installed, skipping it...
 		Removing bundle: test-bundle1
 		Deleting bundle files...
-		Total deleted files: 5
+		Total deleted files: 6
 		Failed to remove 1 of 2 bundles
 	EOM
 	)
 	assert_is_output --identical "$expected_output"
-	# TODO(castulo): The total deleted files should have been 6, change once bug #690 is fixed
 
 }
 
@@ -183,15 +184,15 @@ global_teardown() {
 	# bundle2 was not removed
 	assert_file_exists "$TARGETDIR"/usr/share/clear/bundles/test-bundle2
 	assert_file_exists "$TARGETDIR"/bat/test-file4
+	assert_file_exists "$TARGETDIR"/bat/common
 	expected_output=$(cat <<-EOM
 		Warning: Bundle "fake-bundle" is not installed, skipping it...
 		Removing bundle: test-bundle1
 		Deleting bundle files...
-		Total deleted files: 5
+		Total deleted files: 6
 		Failed to remove 1 of 2 bundles
 	EOM
 	)
 	assert_is_output --identical "$expected_output"
-	# TODO(castulo): The total deleted files should have been 6, change once bug #690 is fixed
 
 }
diff --git a/test/functional/bundleremove/remove-boot-file.bats b/test/functional/bundleremove/remove-boot-file.bats
index ea60555c..4e524003 100755
--- a/test/functional/bundleremove/remove-boot-file.bats
+++ b/test/functional/bundleremove/remove-boot-file.bats
@@ -22,11 +22,10 @@ test_setup() {
 	assert_dir_exists "$TARGETDIR"/usr/
 	expected_output=$(cat <<-EOM
 		Deleting bundle files...
-		Total deleted files: 2
+		Total deleted files: 3
 		Successfully removed 1 bundle
 	EOM
 	)
 	assert_is_output "$expected_output"
-	# TODO(castulo): The total deleted files should have been 3, change once bug #690 is fixed
 
 }