PyCharm Indexing Stuck? 7 Safe Fixes (Exclude, Clear Cache, Repair IDE)

Last updated: September 21, 2025 · Complete solutions for when PyCharm's Indexing… won't finish

Quick Fix Summary

1. Exclude heavy folders — Mark node_modules, .venv, etc. as Excluded
2. Invalidate caches — Run File | Invalidate Caches and select Invalidate and Restart
3. Manual cleanup — Close IDE and delete system caches folder
4. Check plugins — Disable third-party plugins and restart

Table of Contents · Problem Symptoms · Method 1: Exclude Folders · Method 2: Clear Cache · Method 3: Manual Cleanup · Method 4: Check Plugins · Image Guide · Advanced Troubleshooting · Prevention Tips · FAQ

Stuck with PyCharm's Indexing… indicator spinning endlessly at the top of your IDE? This guide provides proven solutions in a safe order. Most cases are resolved simply by running Invalidate Caches and excluding unnecessary folders.

Problem Symptoms

You're likely experiencing indexing issues if you notice:

• Indexing… progress indicator running for 30+ minutes
• Code completion, navigation, and refactoring not working
• High CPU usage or excessive disk I/O
• Project contains large folders like node_modules, .venv, etc.

Method 1: Exclude Unnecessary Folders

Remove heavy folders from indexing scope to reduce processing time.

Steps

1. Right-click the folder in the Project view
2. Select Mark Directory as → Excluded
3. The folder will be marked with the Excluded icon in the Project view

Recommended Folders to Exclude

• node_modules — Node.js dependencies
• .venv, venv — Python virtual environments
• .mypy_cache, .pytest_cache — Python caches
• build, dist — Build artifacts
• logs, temp — Logs and temporary files

Note: VCS metadata like .git normally doesn’t need manual exclusion.

Method 2: Invalidate Caches and Restart

Reset corrupted indexes. This is typically the safest and most effective approach.

Steps

1. Go to File | Invalidate Caches
2. Click Invalidate and Restart
3. PyCharm restarts and begins fresh indexing

This screenshot shows the macOS UI. Source: JetBrains Official Documentation

Method 3: Manual System Cache Cleanup (Advanced)

Try built-in actions first: File | Invalidate Caches… → Help | Delete Leftover IDE Directories. If the issue persists, completely close PyCharm, then delete the system cache directory (.../PyCharm<version>/caches).

Steps

1. Close PyCharm completely (end all related processes)
2. Delete the caches folder from the system directory path
3. Restart PyCharm → Verify new index creation

System directory paths

Windows

%LOCALAPPDATA%\JetBrains\PyCharm<version>\caches

macOS

~/Library/Caches/JetBrains/PyCharm<version>/caches

Linux

~/.cache/JetBrains/PyCharm<version>/caches

Method 4: Check for Plugin Conflicts

Third-party plugins can interfere with indexing. Temporarily disable them to isolate the cause.

Steps

1. Navigate to File | Settings | Plugins
2. Check the Installed tab for third-party plugins
3. Disable suspicious plugins and restart the IDE
4. If the problem disappears, re-enable plugins one by one to identify the culprit

Plugin Types That May Cause Issues

• Heavy file watchers or custom indexing extensions
• Large log/trace processors
• Code analysis/quality tools running on save
• DB/remote sync tooling that scans metadata frequently

Image Capture Guide

Recommended Capture Settings

• Keywords: PyCharm Invalidate Caches Restart dialog, PyCharm indexing progress
• Capture Point: Full File | Invalidate Caches dialog (including button text)
• Screen Scale: 100% recommended (for text clarity)
• Suggested Filename: pycharm-invalidate-caches-restart
• Usage Location: Method 2: Clear Cache section

Advanced Troubleshooting

Check Memory Settings
Go to Help | Change Memory Settings and increase to the IDE's recommended heap memory value.

Restructure Project
Verify the project root is correct and external libraries/build artifacts aren’t mixed in.

Use Repair IDE
Go to File | Repair IDE and follow the steps (refresh VFS → rescan project indexes). Stop if the issue is resolved.

Prevention Tips

Regular Maintenance

• Exclude unnecessary folders when creating new projects
• Keep large logs/build artifacts in separate directories
• Disable or remove unused plugins

Project Setup Recommendations

• Sync .gitignore entries with Excluded folders
• Create virtual environments (.venv) outside the project or exclude them
• Consider using Shared Indexes to reduce initial indexing time

Frequently Asked Questions

Q. Will excluding folders affect deployment or Git?

A. No. It only excludes them from IDE indexing and navigation.

Q. Is it normal for indexing to take a long time after cache deletion?

A. Yes. Depending on project size and disk performance, it can take minutes to hours. Subsequent indexing is much faster.

Q. Is Method 2 sufficient? Do I really need manual deletion?

A. Most cases are resolved with Invalidate Caches. Manual deletion is last resort.

Q. Can I completely disable indexing?

A. Not recommended. Core features like completion and navigation depend on indexing. Instead, optimize scope by exclusions.

Q. After invalidating caches, why did my Local History or custom settings disappear?

A. Local History and some settings are stored in the system cache. If removed, they reset. Back up key configs before deletion.

Related Documentation

1. PyCharm Official Documentation - Indexing Guide
2. PyCharm Official Documentation - IDE Directory Structure
3. PyCharm Official Documentation - Cache Cleanup
4. PyCharm Performance Optimization Guide
5. PyCharm Official Documentation - Repair IDE

If this guide helped you, bookmark it and share with colleagues facing similar issues!