diff --git a/app/assets/javascripts/ide/stores/mutations.js b/app/assets/javascripts/ide/stores/mutations.js
index 1eda576870991de83508847f42613a653d64da51..56a8d9430c701b07e65074d2f0746326b88c59af 100644
--- a/app/assets/javascripts/ide/stores/mutations.js
+++ b/app/assets/javascripts/ide/stores/mutations.js
@@ -200,6 +200,7 @@ export default {
   },
   [types.DELETE_ENTRY](state, path) {
     const entry = state.entries[path];
+    const { tempFile = false } = entry;
     const parent = entry.parentPath
       ? state.entries[entry.parentPath]
       : state.trees[`${state.currentProjectId}/${state.currentBranchId}`];
@@ -209,7 +210,11 @@ export default {
     parent.tree = parent.tree.filter(f => f.path !== entry.path);
 
     if (entry.type === 'blob') {
-      state.changedFiles = state.changedFiles.concat(entry);
+      if (tempFile) {
+        state.changedFiles = state.changedFiles.filter(f => f.path !== path);
+      } else {
+        state.changedFiles = state.changedFiles.concat(entry);
+      }
     }
   },
   [types.RENAME_ENTRY](state, { path, name, entryPath = null }) {
diff --git a/changelogs/unreleased/ide-delete-new-files-state.yml b/changelogs/unreleased/ide-delete-new-files-state.yml
new file mode 100644
index 0000000000000000000000000000000000000000..500115d19d08d8b2b29c9afa2e30596d83fb7af4
--- /dev/null
+++ b/changelogs/unreleased/ide-delete-new-files-state.yml
@@ -0,0 +1,5 @@
+---
+title: Fixed IDE deleting new files creating wrong state
+merge_request:
+author:
+type: fixed
diff --git a/spec/javascripts/ide/stores/mutations_spec.js b/spec/javascripts/ide/stores/mutations_spec.js
index 1e836dbc3f90d2b7422bc2924ddda05f81980f27..6ce76aaa03b425b059256f48686dec3248da67c9 100644
--- a/spec/javascripts/ide/stores/mutations_spec.js
+++ b/spec/javascripts/ide/stores/mutations_spec.js
@@ -213,6 +213,33 @@ describe('Multi-file store mutations', () => {
 
       expect(localState.changedFiles).toEqual([localState.entries.filePath]);
     });
+
+    it('does not add tempFile into changedFiles', () => {
+      localState.entries.filePath = {
+        deleted: false,
+        type: 'blob',
+        tempFile: true,
+      };
+
+      mutations.DELETE_ENTRY(localState, 'filePath');
+
+      expect(localState.changedFiles).toEqual([]);
+    });
+
+    it('removes tempFile from changedFiles when deleted', () => {
+      localState.entries.filePath = {
+        path: 'filePath',
+        deleted: false,
+        type: 'blob',
+        tempFile: true,
+      };
+
+      localState.changedFiles.push({ ...localState.entries.filePath });
+
+      mutations.DELETE_ENTRY(localState, 'filePath');
+
+      expect(localState.changedFiles).toEqual([]);
+    });
   });
 
   describe('UPDATE_FILE_AFTER_COMMIT', () => {