PyCharm “Cannot Connect to Already Running IDE Instance” Error: The Fix That Actually Saves Your Settings

You start PyCharm and get hit with the message “Cannot connect to already running IDE instance.” The common advice is to delete your entire JetBrains folder, but that wipes keymaps, themes, plugins, and months of customization. There’s a faster, safer fix that preserves your settings.

How to properly configure your Python development environment →

Why This Error Happens (And Why the Common Fix Is Garbage)

PyCharm uses lock files and port tokens to prevent multiple instances. If the IDE crashes or is force-quit, stale lock files can remain and block startup. The fix isn’t deleting your entire profile—it’s removing the corrupted cache.

On macOS, the path often looks like ~/Library/Application Support/JetBrains/PyCharmCE2023.2/. Inside, you’ll see subfolders:

• config/ – Settings, keymaps, themes, inspection profiles
• system/ – Caches, indexes, and lock files (the usual culprit)
• plugins/ – Installed plugins
• log/ – Diagnostic logs

Nuking the whole version folder “works,” but it’s overkill. It forces you to rebuild configuration, reinstall plugins, recreate keymaps, and redo interpreters—just to fix one bad cache.

The Surgical Fix: Isolate the Problem Without Losing Everything

Step 1: Get to the Hidden JetBrains Folder

Mac: ~/Library/Application Support/JetBrains/ (use Finder → Go → hold Option → Library, or Cmd+Shift+G and paste the path)

Windows: C:\Users\[USERNAME]\AppData\Roaming\JetBrains\PyCharmCE2023.2 (enable hidden items in File Explorer)

Linux: ~/.config/JetBrains/PyCharmCE2023.2/ (enable “Show Hidden Files” in your file manager)

Step 2: Rename Subfolders to Test

• Quit PyCharm completely.
• Rename system/ to system-OLD.
• Launch PyCharm. If it starts, you’ve found the culprit. PyCharm rebuilds system/ automatically.
• If the error persists, revert and try renaming plugins/, then config/ (rarely the issue).

Common offenders include port.lock and token files in system/. Crashes leave them orphaned.

Step 3: Check That Everything Works

• Recent projects should appear and your settings remain intact (as long as you didn’t rename config/).
• Indexes will rebuild once; performance returns after this initial pass.
• After confirming, you can delete system-OLD (it’s just cache).

Good to know…

Each JetBrains IDE (IntelliJ, WebStorm, PyCharm) maintains separate configuration folders. Fixing or deleting PyCharm’s cache/config won’t affect your other JetBrains tools.

Alternative Approaches (When Renaming Isn’t Enough)

Kill Zombie Processes

Mac/Linux: find with ps aux | grep pycharm and kill with kill -9 [PID]. Windows: use Task Manager (Ctrl+Shift+Esc) → Details tab → End Task.

Release the Port Manually

PyCharm may use ports 6942 or 63342. Check with lsof -i :6942 or lsof -i :63342 and kill the offending PID if it isn’t PyCharm.

The Official Nuclear Option

If nothing works: try File → Invalidate Caches (if you can launch in safe mode). Otherwise, export settings (File → Manage IDE Settings → Export Settings), then delete the entire version folder. You’ll keep settings if you reimport, but plugins and interpreters may need reconfiguration.

Warning…

If you recently updated macOS, app permissions may have changed. If the error resurfaces, check System Settings → Privacy & Security → Full Disk Access and ensure PyCharm is allowed.

Preventing This From Happening Again

• Close PyCharm via File → Exit (or PyCharm → Quit on Mac) to clean up locks.
• Enable Settings Sync: Settings → Settings Sync → Enable, so your configuration is backed up.
• Export settings after major changes: File → Manage IDE Settings → Export Settings.
• Keep old version folders briefly after upgrades; delete once stable.
• After macOS updates, recheck Full Disk Access if issues reappear.

Bottom Line

This error is usually a corrupted cache in system/. Rename that folder, let PyCharm rebuild it, and you’re back up in minutes—with your config and plugins intact. Escalate only if necessary.