diff --git a/app/assets/javascripts/ide/stores/actions.js b/app/assets/javascripts/ide/stores/actions.js
index 5429b834708..48aabaf9dcf 100644
--- a/app/assets/javascripts/ide/stores/actions.js
+++ b/app/assets/javascripts/ide/stores/actions.js
@@ -208,10 +208,6 @@ export const deleteEntry = ({ commit, dispatch, state }, path) => {
 
   commit(types.DELETE_ENTRY, path);
 
-  if (entry.parentPath && state.entries[entry.parentPath].tree.length === 0) {
-    dispatch('deleteEntry', entry.parentPath);
-  }
-
   dispatch('triggerFilesChange');
 };
 
diff --git a/changelogs/unreleased/60860-keep-empty-folders-in-tree.yml b/changelogs/unreleased/60860-keep-empty-folders-in-tree.yml
new file mode 100644
index 00000000000..237d0fd6aef
--- /dev/null
+++ b/changelogs/unreleased/60860-keep-empty-folders-in-tree.yml
@@ -0,0 +1,5 @@
+---
+title: Keep the empty folders in the tree
+merge_request: 29196
+author:
+type: fixed
diff --git a/spec/javascripts/ide/stores/actions_spec.js b/spec/javascripts/ide/stores/actions_spec.js
index 37354283cab..537152f5eed 100644
--- a/spec/javascripts/ide/stores/actions_spec.js
+++ b/spec/javascripts/ide/stores/actions_spec.js
@@ -492,6 +492,33 @@ describe('Multi-file store actions', () => {
         done,
       );
     });
+
+    it('does not delete a folder after it is emptied', done => {
+      const testFolder = {
+        type: 'tree',
+        tree: [],
+      };
+      const testEntry = {
+        path: 'testFolder/entry-to-delete',
+        parentPath: 'testFolder',
+        opened: false,
+        tree: [],
+      };
+      testFolder.tree.push(testEntry);
+      store.state.entries = {
+        testFolder,
+        'testFolder/entry-to-delete': testEntry,
+      };
+
+      testAction(
+        deleteEntry,
+        'testFolder/entry-to-delete',
+        store.state,
+        [{ type: types.DELETE_ENTRY, payload: 'testFolder/entry-to-delete' }],
+        [{ type: 'burstUnusedSeal' }, { type: 'triggerFilesChange' }],
+        done,
+      );
+    });
   });
 
   describe('renameEntry', () => {