How to Fix Git Ignoring .gitignore File

The .gitignore file is one of the most important tools in keeping your Git repositories clean, organized, and free from unnecessary clutter. It helps you prevent unwanted files—such as logs, environment files, temporary build artifacts, compiled assets, IDE-specific files, and caches—from being tracked.

However, there are times when Git appears to ignore your .gitignore rules, even though the patterns are correct. This can be confusing, especially for beginners, but the issue is extremely common and easy to solve once you understand how Git tracking works.

In this guide, we’ll explore why Git sometimes ignores your .gitignore file, how Git’s tracking system behaves, and how to correctly remove previously tracked files. We’ll also walk through global ignore files, pattern mistakes, branch mismatches, cache resetting, and advanced troubleshooting.

Why Git Ignores Your .gitignore File

Before diving into the fix, it’s important to understand why this happens. Git only ignores files that are not already being tracked. If a file was committed before adding it to .gitignore, Git will continue to track it—even if it appears in your ignore file.

Here are the most common reasons Git ignores your .gitignore file:

1. The File Was Already Tracked Before You Added It to .gitignore

This is the #1 cause.

Example:

• You commit config.php

• Later, you add config.php to .gitignore

• Git will still track this file because it is already in the repository’s history

Git’s logic is:

“A tracked file stays tracked unless explicitly removed.”

2. .gitignore Changes Were Made on Another Branch

You may have updated .gitignore on branch A but are working on branch B. Your changes are not active in your current branch.

3. Incorrect Patterns or Typos Inside .gitignore

Examples of incorrect patterns:

/node_modules wrong node_modules/ correct

Or:

.env.example if you meant .env .env correct

4. A Global Git Ignore File Overrides Your Local One

Git supports global ignore rules, which may conflict with project-level rules.

Check if you have one:

git config --get core.excludesfile

This file may be ignoring or overriding patterns unintentionally.

5. System-Level Git Ignore Settings

On Linux/macOS systems, sometimes system-wide Git ignore files exist in:

/etc/gitconfig ~/.config/git/ignore

These can override your local .gitignore.

STEP-BY-STEP FIX: Make Git Respect Your .gitignore File

Now let’s fix the problem properly.

Step 1: Verify Your .gitignore Rules

Ensure your patterns are correct. Here are common examples:

Ignore a file:

secret.txt

Ignore a folder:

node_modules/ storage/logs/ vendor/

Ignore all environment files:

.env .env.*

Ignore all log files:

*.log

Reference guide:
https://git-scm.com/docs/gitignore

Step 2: Remove Previously Tracked Files from Git

This is the most important part.

Even if .gitignore is correct, Git will continue tracking files that were previously committed.

To force Git to stop tracking them:

Run:

git rm -r --cached .

This removes all tracked files from the Git index (staging area) without deleting them from your working directory.

Your files remain safe locally.

Step 3: Re-add Everything (Respecting .gitignore)

Now run:

git add .

Git will only add files not ignored by .gitignore.

Step 4: Commit the Cleanup

git commit -m "Fix .gitignore and remove ignored files"

This updates your history with the corrected file tracking.

Step 5: Push Changes Back to the Repository

git push origin <branch>

Replace <branch> with your current branch name:

• main

• master

• dev

• feature-x

This updates the remote repo to match your corrected ignore rules.

Important Warning

If you're working on a shared repository, tell your team before pushing large history modifications. Removing files from the index affects everyone.

Advanced Troubleshooting

If Git still ignores your .gitignore rules, here are more things to check.

1. Test What Git Ignores

Run:

git check-ignore -v <filename>

Git will tell you why a file is ignored and which rule is causing it.

2. Clear Git Cache Manually

git rm --cached <file>

This is helpful when only specific files are behaving incorrectly.

3. Ensure .gitignore Has Correct Line Endings

On Windows systems, CRLF issues may cause .gitignore to misbehave.

4. Ensure .gitignore Is Not Named Wrong

Common mistakes:

.gitignore.txt .gitignore .txt gitignore

It must be exactly:

.gitignore

5. Verify Git Doesn't Have Local Include Files

Check:

git config --get-all core.excludesfile

If another ignore file exists, review its patterns.

Best Practices for Managing .gitignore

• Always commit .gitignore early in the project

• Use clear, organized sections inside .gitignore

• Use global ignore file for IDE files (like .idea, .vscode)

• Never ignore essential files such as composer.json

• Avoid committing environment or credential files (.env)

Conclusion

When Git ignores your .gitignore file, it's almost always because the files were already tracked before being added to the ignore list. By clearing the cache using git rm --cached, re-adding files, and committing the changes, you ensure Git properly respects your ignore rules moving forward.

With the right understanding of .gitignore, Git tracking behavior, and the troubleshooting steps outlined above, you can maintain a clean, efficient, and professional repository—free from unnecessary clutter.

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