Fixing 'fatal: bad config file' and malformed .git/config in Git

What this error means

Git failed to parse a config file. You’ll see messages like:

• fatal: bad config file at: /path/to/.git/config: line 12
• error: malformed config file in: ~/.gitconfig

The fix is to identify the broken file and correct its syntax or encoding.

Where Git reads config

• Local (repo): .git/config
• Global (user): ~/.gitconfig (Windows: %USERPROFILE%.gitconfig)
• System: $(git --exec-path)/../etc/gitconfig or platform-specific etc/gitconfig

Tip: Git merges these; one bad file breaks all Git commands.

Quickstart: fix in 60 seconds

1. Note the file and line number from the error.
2. Back up the file.
3. Open and fix obvious syntax: section headers, quotes, or conflict markers.
4. Save as UTF-8 without BOM; ensure Unix/Windows line endings are consistent.
5. Validate by listing config.

Minimal commands:

# 1) Back up
cp .git/config .git/config.bak 2>/dev/null || true
cp ~/.gitconfig ~/.gitconfig.bak 2>/dev/null || true

# 2) Try to list while bypassing other scopes (helps isolate)
GIT_CONFIG_SYSTEM=/dev/null GIT_CONFIG_GLOBAL=/dev/null git config --file .git/config --list --show-origin || true
GIT_CONFIG_SYSTEM=/dev/null git config --global --list --show-origin || true

# 3) Validate once fixed
git config --list --show-origin

If Git refuses to run due to a broken global config, temporarily bypass it:

GIT_CONFIG_GLOBAL=/dev/null git status

Minimal working example (.git/config)

If your local config is badly broken, replace it with a minimal, valid file and re-add settings.

[core]
	repositoryformatversion = 0
	filemode = true
	bare = false
	logallrefupdates = true
[user]
	name = Jane Doe
	email = [email protected]
[remote "origin"]
	url = [email protected]:org/repo.git
	fetch = +refs/heads/*:refs/remotes/origin/*

Then validate:

git config --list --show-origin

Common causes and fixes

1. Missing or malformed section headers

• Symptom: lines outside [section] blocks.
• Fix: ensure settings live under headers like [core], [user], [remote "origin"].

Bad:

user.name = Jane
user.email = [email protected]

Good:

[user]
	name = Jane
	email = [email protected]

1. Unbalanced quotes/brackets in section names

• Symptom: [remote "origin] or [remote origin"]
• Fix: use paired quotes around the name.

Good:

[remote "origin"]
	url = [email protected]:org/repo.git

1. Bad include/includeIf lines

• Symptom: include.path without a value or malformed condition.
• Fix: quote the condition and provide a valid path.

Good:

[include]
	path = ~/.gitconfig-common
[includeIf "gitdir:~/work/"]
	path = ~/.gitconfig-work

1. Merge conflict markers accidentally committed to config

• Symptom: lines starting with <<<<<<<, =======, >>>>>>>.
• Fix: remove markers and keep the intended settings.

1. Encoding issues (BOM, UTF-16)

• Symptom: saved as UTF-16/UTF-8 with BOM; Git can’t parse.
• Fix: save as UTF-8 without BOM. On Unix-like systems:

# Strip UTF-8 BOM (GNU sed)
sed -i '1s/^\xEF\xBB\xBF//' ~/.gitconfig

# Or rewrite as UTF-8 without BOM via iconv
iconv -f utf-8 -t utf-8 ~/.gitconfig > ~/.gitconfig.nobom && mv ~/.gitconfig.nobom ~/.gitconfig

1. Stray characters or tabs vs. spaces

• Git accepts tabs/spaces, but stray non-printable characters can break parsing. Remove any odd characters.

Step-by-step repair workflow

1. Identify the failing file

• Read Git’s error; it usually names the file and line.

1. Back up

cp /path/to/file /path/to/file.bak

1. Fix syntax in an editor

• Ensure every key is key = value under a valid [section].
• Quote names in subsection headers: [remote "name"].
• Remove conflict markers.
• Correct include/includeIf lines.
• Save as UTF-8 without BOM.

1. Validate

git config --list --show-origin

If still failing, narrow scope:

GIT_CONFIG_SYSTEM=/dev/null GIT_CONFIG_GLOBAL=/dev/null git config --file .git/config --list
GIT_CONFIG_NOSYSTEM=1 git config --global --list

Recreate a fresh local config

If .git/config is beyond repair:

mv .git/config .git/config.broken
# Reinitialize to regenerate minimal structure
git init
# Re-add remote and essentials
git remote add origin [email protected]:org/repo.git
git config user.name "Your Name"
git config user.email "[email protected]"

Pitfalls to avoid

• Editing with tools that save UTF-16 or add BOMs.
• Copy-pasting from rich text; it may insert smart quotes or non-breaking spaces.
• Typos in includeIf conditions (must be like "gitdir:PATH/").
• Comment syntax: use # or ; at line start; inline comments after values can be risky.
• Mixing multiple conflicting definitions; last one wins but can be confusing.

Performance notes

• Many nested include files slow startup slightly; consolidate where possible.
• Keep config small and relevant to your workflow.
• Prefer includes for rarely used settings to avoid parsing large files on every command.

FAQ

Q: Where are my config files? A: Local: .git/config in the repo. Global: ~/.gitconfig (Windows: %USERPROFILE%.gitconfig). System: platform gitconfig in etc.

Q: Git won’t run because my global file is broken. How can I work? A: Temporarily bypass it: GIT_CONFIG_GLOBAL=/dev/null git <cmd>. Then fix ~/.gitconfig.

Q: Can I delete .git/config? A: Yes, but back it up first. Run git init to recreate basics, then re-add remotes and settings.

Q: How do I validate after fixing? A: Run git config --list --show-origin. It should print all settings without errors.

Q: Do CRLF line endings matter? A: Git can parse CRLF or LF, but inconsistent encoding (UTF-16/BOM) breaks parsing; prefer UTF-8 without BOM.