How to fix fatal: It seems that there is already a rebase-merge directory, and I wonder if you are in the middle of another rebase in Git

GitBEGINNERLOWUpdated Dec 6, 2025· 236 views

This error occurs when Git detects an incomplete rebase operation. You either need to finish, abort, or skip the existing rebase, or manually remove the leftover .git/rebase-merge directory if no rebase is actually in progress.

Quick fix

Fixes fatal: It seems that there is already a rebase-merge directory, and I wonder if you are in the middle of another rebase

# Check Git status
git status

Check if you have an active rebase
Continue the existing rebase (if you want to finish it)
Abort the existing rebase (if you want to undo it)
Skip the current commit (if a single commit is problematic)

git — error

$# Check Git status
git status
fatal: It seems that there is already a rebase-merge directory, and I wonder if you are in the middle of another rebase

What this error means

When you run a Git rebase command, Git creates a `.git/rebase-merge` directory to store the state of the ongoing rebase operation. This includes information about which commits are being rebased, the original branch position, and any conflict resolution progress. The error "It seems that there is already a rebase-merge directory" means Git found this directory when you tried to start a new rebase. Git interprets this as a sign that you're already in the middle of a rebase operation. This situation typically occurs in one of two scenarios: 1. **You are genuinely in the middle of a rebase** - perhaps you encountered a merge conflict, resolved it, but forgot to run `git rebase --continue`, or you simply got distracted and never finished the rebase. 2. **A previous rebase was interrupted** - the rebase process was killed (e.g., by closing the terminal, a system crash, or a Git GUI tool crashing), leaving behind a "phantom" rebase-merge directory with no actual rebase in progress. Git cannot automatically determine which scenario applies, so it asks you to investigate and resolve the situation.

Typical symptoms

Git rebase command fails immediately with 'rebase-merge directory already exists' message
Git suggests running 'git rebase --continue', '--abort', or '--skip'
The error appears even though you don't remember starting a rebase
Git GUI tools (GitKraken, VS Code GitLens, SourceTree) show errors about ongoing rebase
Running 'brew update' fails with this error (Homebrew uses Git internally)
Cannot start an interactive rebase with 'git rebase -i'

Common causes

A previous rebase was interrupted before completion (terminal closed, system crashed, etc.)
You started a rebase, encountered conflicts, but never completed it with --continue or --abort
A Git GUI tool crashed during a rebase operation
Running multiple Git operations in parallel that conflict with each other
Network interruption during a remote rebase operation
The rebase-merge directory was corrupted by filesystem issues

How to fix "fatal: It seems that there is already a rebase-merge directory, and I wonder if you are in the middle of another rebase"

1Check if you have an active rebase

First, determine whether you actually have a rebase in progress:

bash

# Check Git status
git status

If a rebase is in progress, you'll see a message like:

bash

rebase in progress; onto abc1234
You are currently rebasing branch 'feature' on 'abc1234'.

If you don't see this message but still get the error, you have a "phantom" rebase-merge directory (skip to step 5).

2Continue the existing rebase (if you want to finish it)

If you have unfinished rebase work and want to complete it:

bash

# If there were conflicts, resolve them first in your editor
# Then mark the conflicts as resolved
git add <conflicted-files>

# Continue the rebase
git rebase --continue

Repeat this process for each commit that has conflicts until the rebase completes.

3Abort the existing rebase (if you want to undo it)

If you want to cancel the rebase and return to the state before it started:

bash

git rebase --abort

This will:
- Stop the rebase operation
- Reset your branch to where it was before the rebase began
- Remove the .git/rebase-merge directory

Your working directory will be restored to its pre-rebase state.

4Skip the current commit (if a single commit is problematic)

If you're in a rebase and one particular commit is causing issues that you want to skip:

bash

git rebase --skip

Warning: This will discard the changes from the current commit being applied. Only use this if you're certain you don't need those changes. The commit will not be included in your rebased branch.

5Manually remove the rebase-merge directory (phantom rebase)

If git status doesn't show an active rebase but the error persists, the directory is leftover from an interrupted operation. You can safely remove it:

bash

# Remove the phantom rebase-merge directory
rm -rf .git/rebase-merge

After removing the directory, verify your repository is in a clean state:

bash

git status

You should now be able to start a new rebase operation.

6Use git rebase --quit (alternative cleanup)

Git also provides a built-in command to clean up the rebase state:

bash

git rebase --quit

This is similar to --abort but doesn't reset HEAD to the original branch. It simply removes the rebase state files. This is useful if your repository is in an inconsistent state where --abort might fail.

Note: If you used --autostash when starting the rebase, the stashed changes will be lost with --quit. Check .git/rebase-merge/autostash for the stash commit hash before running this command if you need to recover those changes.

7Fix for Homebrew users

If you encounter this error when running brew update, Homebrew provides a dedicated fix:

bash

# Homebrew's built-in reset command
brew update-reset

Alternatively, you can manually fix Homebrew's Git repository:

bash

# Navigate to Homebrew directory and abort the rebase
cd $(brew --repository)
git rebase --abort
brew update

On Apple Silicon Macs, the Homebrew directory is typically /opt/homebrew. On Intel Macs, it's /usr/local/Homebrew.

Advanced notes

### Understanding the .git/rebase-merge Directory

The .git/rebase-merge directory contains several files that Git uses to track the rebase state:

- head-name: The name of the branch being rebased
- onto: The commit you're rebasing onto
- orig-head: The original HEAD position before the rebase
- msgnum: The current commit number being processed
- end: The total number of commits to rebase
- interactive: Present if this is an interactive rebase
- autostash: Contains the stash commit hash if --autostash was used

### Rebase-Merge vs Rebase-Apply

Git uses two different mechanisms for rebasing:
- .git/rebase-merge: Used for interactive rebases (git rebase -i) and standard rebases
- .git/rebase-apply: Used when applying patches with git am or older rebase implementations

If you see an error about rebase-apply instead, the same solutions apply - just reference that directory instead.

### Recovering from a Corrupted Rebase State

If your rebase state is corrupted and normal commands don't work:

bash

# Check the reflog to see recent operations
git reflog

# Find the commit hash before the rebase started
# Then reset to that state
git reset --hard <commit-hash>

# Remove the corrupted rebase directory
rm -rf .git/rebase-merge

### Preventing This Error

To avoid leaving orphan rebase directories:
1. Always complete rebases with --continue, --abort, or --skip
2. Avoid closing terminals or interrupting Git operations
3. If using Git GUIs, ensure they close cleanly
4. Consider using git pull --rebase carefully in automated scripts

Frequently asked questions

What does "fatal: It seems that there is already a rebase-merge directory, and I" mean?: git/rebase-merge directory to store the state of the ongoing rebase operation. This includes information about which commits are being rebased, the original branch position, and any conflict resolution progress. The error "It seems that there is already a rebase-merge directory" means Git found this directory when you tried to start a new rebase.
How do I fix "fatal: It seems that there is already a rebase-merge directory, and I"?: This error occurs when Git detects an incomplete rebase operation. You either need to finish, abort, or skip the existing rebase, or manually remove the leftover .git/rebase-merge directory if no rebase is actually in progress.
What causes "fatal: It seems that there is already a rebase-merge directory, and I"?: A previous rebase was interrupted before completion (terminal closed, system crashed, etc.) You started a rebase, encountered conflicts, but never completed it with --continue or --abort A Git GUI tool crashed during a rebase operation
Is the "fatal: It seems that there is already a rebase-merge directory, and I" error serious?: It is a low-severity error — more of a blocker than a risk. The steps above resolve it.

Official resources & further reading

📚Git Official Documentation
📖
Git - git-rebase Documentation(Official Docs)
📖
Git Branching - Rebasing(Official Docs)
💬
How fix 'fatal: It seems that there is already a rebase-merge directory' - Stack Overflow(Stack Overflow)
💬
Forgotten rebase interactive - git - Stack Overflow(Stack Overflow)
🐙
Phantom rebase-merge directory - GitLens Issue(GitHub)
📖
git rebase - Atlassian Git Tutorial(Official Docs)

How to fix fatal: It seems that there is already a rebase-merge directory, and I wonder if you are in the middle of another rebase in Git

Quick fix

What this error means

Typical symptoms

Common causes

How to fix "fatal: It seems that there is already a rebase-merge directory, and I wonder if you are in the middle of another rebase"

Advanced notes

Frequently asked questions

Related errors

Official resources & further reading