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How to Clean Up Your Claude Code MCP Servers: A Practical Guide

Cowrie
Cowrie
Dev @ Bswen

Problem

When I first set up Claude Code, I kept adding MCP servers. Someone on Reddit recommended a search MCP, then I saw a Twitter post about an Obsidian connector, and before I knew it—I had 20 MCP servers running in the background. My setup felt sluggish, and I had no idea what half of these servers actually did.

Sound familiar?

What happened?

I started with good intentions. Every time I saw someone recommend an MCP server—“you need this for API docs,” “this one connects to your database”—I installed it. “Just in case,” I told myself.

After a few months, my Claude Code felt slow. Responses took longer. The context window seemed to fill up faster. I had no idea what was causing it until I checked my MCP configuration.

Here’s what I found:

  • 3 different search MCPs (did I really need all three?)
  • 2 duplicate Obsidian connectors (installed twice by accident?)
  • 1 Postgres server I never once used
  • Various MCPs I added for projects that never happened

Total: 20 MCP servers. How many did I actually use? 5.

How to solve it?

I decided to do a cleanup. Here’s what I did:

Step 1: Find your MCP config file

The config is typically in your Claude Code settings. Look for the MCP servers section.

Step 2: List everything

Go through each MCP server and ask yourself:

  • Have I used this in the last 30 days?
  • Do I actually need this for my current work?
  • Is there a duplicate doing the same thing?

Step 3: Archive, don’t delete

I didn’t delete anything right away. I moved unused MCPs to a backup file. This way, if I actually needed one later, I could restore it.

Step 4: Test and verify

After removing 15 out of 20 MCP servers, I tested Claude Code. The difference was noticeable—faster responses, cleaner context, less overhead.

The reason

I think the key reason this matters is:

  • Context window competition: Each MCP server shares your context window
  • Startup overhead: More MCPs mean longer initialization time
  • Potential conflicts: Duplicate MCPs can interfere with each other
  • Token waste: Unused MCPs still get loaded into context

Summary

In this post, I showed how I cleaned up my Claude Code MCP servers. The key point is to regularly audit your MCP servers, remove duplicates and anything you haven’t used in the past month, and archive (don’t delete) so you can restore what you actually need.

Final Words + More Resources

My intention with this article was to help others share my knowledge and experience. If you want to contact me, you can contact by email: Email me

Here are also the most important links from this article along with some further resources that will help you in this scope:

Oh, and if you found these resources useful, don’t forget to support me by starring the repo on GitHub!

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