diff --git a/plugins/scaffolder-backend/src/scaffolder/stages/prepare/bitbucket.ts b/plugins/scaffolder-backend/src/scaffolder/stages/prepare/bitbucket.ts
index 8ee39f41fa..5bc58e34f0 100644
--- a/plugins/scaffolder-backend/src/scaffolder/stages/prepare/bitbucket.ts
+++ b/plugins/scaffolder-backend/src/scaffolder/stages/prepare/bitbucket.ts
@@ -20,7 +20,10 @@ import { TemplateEntityV1alpha1 } from '@backstage/catalog-model';
 import { parseLocationAnnotation } from '../helpers';
 import { InputError, Git } from '@backstage/backend-common';
 import { PreparerBase, PreparerOptions } from './types';
-import { readBitbucketIntegrationConfigs, BitbucketIntegrationConfig } from '@backstage/integration';
+import {
+  readBitbucketIntegrationConfigs,
+  BitbucketIntegrationConfig,
+} from '@backstage/integration';
 import GitUriParser from 'git-url-parse';
 import { Config } from '@backstage/config';
 import { Logger } from 'winston';
@@ -29,16 +32,29 @@ export class BitbucketPreparer implements PreparerBase {
   private readonly privateToken: string;
   private readonly username: string;
   private readonly logger: Logger;
-  private readonly integrations: BitbucketIntegrationConfig[];  
-  constructor(config: Config, { logger }: { logger: Logger}) {
+  private readonly integrations: BitbucketIntegrationConfig[];
+  constructor(config: Config, { logger }: { logger: Logger }) {
     this.logger = logger;
     this.integrations = readBitbucketIntegrationConfigs(
-      config.getOptionalConfigArray('integrations.bitbucket') ??Takj
-    )
+      config.getOptionalConfigArray('integrations.bitbucket') ?? [],
+    );
+
+    if (!this.integrations.length) {
+      this.logger.warn(
+        'Integrations for BitBucket in Scaffolder are not set. This will cause errors in a future release. Please migrate to using integrations config and specifying tokens under hostnames',
+      );
+    }
+
     this.username =
       config.getOptionalString('scaffolder.bitbucket.api.username') ?? '';
     this.privateToken =
       config.getOptionalString('scaffolder.bitbucket.api.token') ?? '';
+
+    if (this.username || this.privateToken) {
+      this.logger.warn(
+        "DEPRECATION: Using the token format under 'scaffolder.github.token' will not be respected in future releases. Please consider using integrations config instead",
+      );
+    }
   }
 
   async prepare(
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,