diff --git a/apps/api/src/services/githubPusher.ts b/apps/api/src/services/githubPusher.ts
index ec038f6..3d4d211 100644
--- a/apps/api/src/services/githubPusher.ts
+++ b/apps/api/src/services/githubPusher.ts
@@ -72,36 +72,19 @@ async function emitProgress(
 }
 
 async function ensureMainBranchExists(octokit: Octokit, owner: string, repo: string): Promise<void> {
-  try {
-    await octokit.repos.getBranch({
-      owner,
-      repo,
-      branch: "main",
-    });
-    return;
-  } catch {
-    // Branch does not exist yet. Initialize it below.
+  // With auto_init the repo is created with an initial commit on `main`, but
+  // GitHub populates it asynchronously. Poll briefly until the branch is
+  // visible before pushing files.
+  for (let attempt = 0; attempt < 10; attempt++) {
+    try {
+      await octokit.repos.getBranch({ owner, repo, branch: "main" });
+      return;
+    } catch {
+      await wait(500);
+    }
   }
 
-  const tree = await octokit.git.createTree({
-    owner,
-    repo,
-    tree: [],
-  });
-
-  const commit = await octokit.git.createCommit({
-    owner,
-    repo,
-    message: "chore: initialize main branch",
-    tree: tree.data.sha,
-  });
-
-  await octokit.git.createRef({
-    owner,
-    repo,
-    ref: "refs/heads/main",
-    sha: commit.data.sha,
-  });
+  throw new Error("Timed out waiting for the 'main' branch to be initialized");
 }
 
 export async function pushToGitHub(
@@ -124,7 +107,7 @@ export async function pushToGitHub(
     name: repoName,
     description: "Generated by StackForge",
     private: false,
-    auto_init: false,
+    auto_init: true,
   });
 
   const owner = repo.data.owner?.login ?? authUser.data.login;
@@ -148,6 +131,23 @@ export async function pushToGitHub(
   }
 
   for (const [filePath, content] of entries) {
+    // The repo was auto-initialized with a README, so updating an existing
+    // file requires its current blob sha. Look it up; absent for new files.
+    let existingSha: string | undefined;
+    try {
+      const existing = await octokit.repos.getContent({
+        owner,
+        repo: repoName,
+        path: filePath,
+        ref: "main",
+      });
+      if (!Array.isArray(existing.data) && "sha" in existing.data) {
+        existingSha = existing.data.sha;
+      }
+    } catch {
+      // File does not exist yet; create it fresh.
+    }
+
     await octokit.repos.createOrUpdateFileContents({
       owner,
       repo: repoName,
@@ -155,6 +155,7 @@ export async function pushToGitHub(
       message: "feat: initial project generated by StackForge",
       content: Buffer.from(content, "utf8").toString("base64"),
       branch: "main",
+      ...(existingSha !== undefined ? { sha: existingSha } : {}),
     });
 
     await emitProgress(onProgress, {