diff --git a/.changeset/purple-days-film.md b/.changeset/purple-days-film.md
new file mode 100644
index 0000000000..09d760c33e
--- /dev/null
+++ b/.changeset/purple-days-film.md
@@ -0,0 +1,5 @@
+---
+'@backstage/plugin-techdocs-node': patch
+---
+
+Fixed bug that prevented deletion of stale files when non-empty directories where tried to be deleted as well.
diff --git a/plugins/techdocs-node/src/stages/publish/helpers.test.ts b/plugins/techdocs-node/src/stages/publish/helpers.test.ts
index fa934d6dd9..7b303b3bf5 100644
--- a/plugins/techdocs-node/src/stages/publish/helpers.test.ts
+++ b/plugins/techdocs-node/src/stages/publish/helpers.test.ts
@@ -158,6 +158,16 @@ describe('getStaleFiles', () => {
     expect(staleFiles).toHaveLength(1);
     expect(staleFiles).toEqual(expect.arrayContaining(['stale_file.png']));
   });
+
+  it('should not return directories as stale files if they are parent directories of new files', () => {
+    const oldFiles = [...defaultFiles, 'default/Component/backstage/foo'];
+    const newFiles = [
+      ...defaultFiles,
+      'default/Component/backstage/foo/bar/index.html',
+    ];
+    const staleFiles = getStaleFiles(newFiles, oldFiles);
+    expect(staleFiles).toHaveLength(0);
+  });
 });
 
 describe('getCloudPathForLocalPath', () => {
diff --git a/plugins/techdocs-node/src/stages/publish/helpers.ts b/plugins/techdocs-node/src/stages/publish/helpers.ts
index decefae187..0b9384dba3 100644
--- a/plugins/techdocs-node/src/stages/publish/helpers.ts
+++ b/plugins/techdocs-node/src/stages/publish/helpers.ts
@@ -169,8 +169,21 @@ export const getStaleFiles = (
   oldFiles: string[],
 ): string[] => {
   const staleFiles = new Set(oldFiles);
+  const removedParentDirs = new Set();
   newFiles.forEach(newFile => {
     staleFiles.delete(newFile);
+
+    // We have to traverse through the directory hierarchy of a new file and
+    // ensure that we won't try to delete one of the parent directories.
+    let parentDir = newFile.substring(0, newFile.lastIndexOf('/'));
+    while (
+      !removedParentDirs.has(parentDir) &&
+      parentDir.length >= newFile.indexOf('/')
+    ) {
+      staleFiles.delete(parentDir);
+      removedParentDirs.add(parentDir);
+      parentDir = parentDir.substring(0, parentDir.lastIndexOf('/'));
+    }
   });
   return Array.from(staleFiles);
 };