diff --git a/.changeset/nervous-mirrors-cough.md b/.changeset/nervous-mirrors-cough.md
new file mode 100644
index 0000000000..da96e49edc
--- /dev/null
+++ b/.changeset/nervous-mirrors-cough.md
@@ -0,0 +1,5 @@
+---
+'@backstage/plugin-scaffolder-backend': patch
+---
+
+bug(scaffolder): Ignore the .git folder when adding dot-files to the index
diff --git a/plugins/scaffolder-backend/src/scaffolder/stages/publish/helpers.ts b/plugins/scaffolder-backend/src/scaffolder/stages/publish/helpers.ts
index 796e48b8f8..ffefb88cf0 100644
--- a/plugins/scaffolder-backend/src/scaffolder/stages/publish/helpers.ts
+++ b/plugins/scaffolder-backend/src/scaffolder/stages/publish/helpers.ts
@@ -39,7 +39,7 @@ export async function initRepoAndPush({
     dir,
   });
 
-  const paths = await globby(['./**', './**/.*'], {
+  const paths = await globby(['./**', './**/.*', '!.git'], {
     cwd: dir,
     gitignore: true,
     dot: true,