diff --git a/src/job/jobHandler.ts b/src/job/jobHandler.ts
index ca616bdac..a48d2ee85 100644
--- a/src/job/jobHandler.ts
+++ b/src/job/jobHandler.ts
@@ -213,7 +213,7 @@ export abstract class JobHandler {
       if (this.currJob.payload.repoName === 'docs-monorepo') {
         await this._fileSystemServices.saveUrlAsFile(
           `https://raw.githubusercontent.com/mongodb/docs-worker-pool/meta/makefiles/Makefile.${this.currJob.payload.project}`,
-          `repos/${this.currJob.payload.project}/Makefile`,
+          `repos/${this.currJob.payload.project}/cloud-docs/Makefile`,
           {
             encoding: 'utf8',
             flag: 'w',
@@ -239,7 +239,7 @@ export abstract class JobHandler {
   public isbuildNextGen(): boolean {
     let workerPath = `repos/${this.currJob.payload.repoName}/worker.sh`;
     if (this.currJob.payload.repoName === 'docs-monorepo')
-      workerPath = `repos/${this.currJob.payload.project}/worker.sh`;
+      workerPath = `repos/${this.currJob.payload.project}/cloud-docs/worker.sh`;
     // const workerPath = `repos/${this.currJob.payload.repoName}/worker.sh`;
     if (this._fileSystemServices.rootFileExists(workerPath)) {
       const workerContents = this._fileSystemServices.readFileAsUtf8(workerPath);
@@ -291,7 +291,9 @@ export abstract class JobHandler {
   private async callWithBenchmark(command: string, stage: string): Promise<CommandExecutorResponse> {
     const start = performance.now();
     const pathToRepo =
-      this.currJob.payload.repoName === 'docs-monorepo' ? `repos/cloud-docs` : `repos/${this.currJob.payload.repoName}`;
+      this.currJob.payload.repoName === 'docs-monorepo'
+        ? `repos/cloud-docs/cloud-docs`
+        : `repos/${this.currJob.payload.repoName}`;
     const resp = await this._commandExecutor.execute([command], pathToRepo);
     // const resp = await this._commandExecutor.execute([command], `repos/${this.currJob.payload.repoName}`);
 
@@ -404,7 +406,7 @@ export abstract class JobHandler {
     }
     let fileToWriteTo = `repos/${this.currJob.payload.repoName}/.env.production`;
     if (this.currJob.payload.repoName === 'docs-monorepo')
-      fileToWriteTo = `repos/${this.currJob.payload.project}/.env.production`;
+      fileToWriteTo = `repos/${this.currJob.payload.project}/cloud-docs/.env.production`;
     this._fileSystemServices.writeToFile(fileToWriteTo, envVars, {
       encoding: 'utf8',
       flag: 'w',
@@ -458,7 +460,7 @@ export abstract class JobHandler {
       this._logger.save(this.currJob._id, 'IN PREP, using cloud-docs');
       this.currJob.buildCommands = [
         `. /venv/bin/activate`,
-        `cd repos/${this.currJob.payload.project}`,
+        `cd repos/${this.currJob.payload.project}/cloud-docs`,
         `rm -f makefile`,
         `make html`,
       ];
diff --git a/src/services/commandExecutor.ts b/src/services/commandExecutor.ts
index 9221cfc51..84dfaea5a 100644
--- a/src/services/commandExecutor.ts
+++ b/src/services/commandExecutor.ts
@@ -100,7 +100,11 @@ export class GithubCommandExecutor extends ShellCommandExecutor implements IGith
     branchName: string,
     newHead: string | null | undefined = null
   ): Promise<CommandExecutorResponse> {
-    const pullRepoCommands = [`cd repos/${repoDirName}`, `git checkout ${branchName}`, `git pull origin ${branchName}`];
+    const pullRepoCommands = [
+      `cd repos/${repoDirName}/cloud-docs`,
+      `git checkout ${branchName}`,
+      `git pull origin ${branchName}`,
+    ];
     if (newHead) {
       pullRepoCommands.push(`git checkout ${newHead} .`);
     }