How to fix error: bad ref for .git/refs/heads/main in Git

First, run git fsck to identify all corrupted references:

git fsck --full

This will list all problematic refs. You can also check the specific file mentioned in the error:

cat .git/refs/heads/main

If the file is corrupted, you'll see null characters, garbage data, or an empty output instead of a 40-character SHA-1 hash.

Git's reflog tracks recent changes to each ref. Check if the correct SHA is preserved:

# View the reflog for the corrupted branch
tail -n 5 .git/logs/refs/heads/main

# Or use git reflog (may fail if HEAD is also corrupted)
git reflog show main

The reflog entries look like this:

abc1234 def5678 User <email> 1234567890 +0000  commit: message

The second SHA (def5678... in full 40-character form) is the most recent commit for that ref.

Once you've identified the correct SHA (or confirmed you can recover from remote), delete the corrupted file:

# Remove the corrupted ref
rm .git/refs/heads/main

# If the logs file is also corrupted, remove it too
rm .git/logs/refs/heads/main

Important: Only delete the specific corrupted files, not the entire refs directory.

If you found the correct SHA in the reflog, restore the branch:

# Replace <sha> with the 40-character SHA from your reflog
git update-ref refs/heads/main <sha>

# Example:
git update-ref refs/heads/main a1b2c3d4e5f6g7h8i9j0k1l2m3n4o5p6q7r8s9t0

Verify the restoration:

git log main --oneline -5

If you can't find the SHA in the reflog, fetch from the remote repository:

# Fetch all refs from origin
git fetch origin

# Recreate the local branch from the remote
git branch -f main origin/main

# Or checkout the branch
git checkout -B main origin/main

This will reset your local branch to match the remote, so any unpushed commits will be lost.

After fixing the refs, clean up the repository:

git gc --prune=now

Then verify everything is working:

git fsck --full
git status

If git fsck reports no errors, your repository is healthy again.

If the corrupted refs were remote tracking branches, prune them:

git remote prune origin

This removes any local references to remote branches that no longer exist.

If multiple refs are corrupted and recovery is difficult, clone a fresh copy:

# Clone the repository fresh
git clone <repository-url> project-fresh

# Copy any uncommitted changes from the old repo
cp -r old-project/src/* project-fresh/src/

# Verify and commit your changes
cd project-fresh
git status
git add .
git commit -m "Recover uncommitted changes"

This approach preserves all committed history from the remote while recovering your local changes.