Let AI Detect and Patch Your Vulnerable Code: Claude Desktop and Snyk MCP Server

Integrating AI assistants into your development workflow can transform how you approach security. Claude Desktop, with its support for the Model Context Protocol (MCP), provides a native interface for connecting to external tools and data sources. One such toolkit is Snyk's official MCP Server, which brings enterprise-grade security scanning directly into your conversations with Claude.

Keep in mind that Claude Desktop is different from Claude Code, though the process of setting that up with Snyk’s Official MCP Server has a lot in common with this flow.

Setting up the official Snyk MCP Server

The Snyk MCP Server is available as part of the Snyk CLI version 1.1298.0 or later. This is the official implementation from Snyk, designed to integrate their comprehensive security scanning capabilities into MCP-enabled environments. A couple of other open source Snyk MCP server implementations exist, leveraging Snyk API keys instead:

• sammcj’s implementation

• punkpeye’s implementation

If you want to obtain an API key, you can create a free account atsnyk.io. But for now, we are just going to use the Official Snyk MCP Server. 

Prerequisites

Before setting up the Snyk MCP Server with Claude Desktop, you'll need:

1. Snyk Account: Create a free account at snyk.io 

2. Claude Desktop: Download and install from claude.ai/download

Installation steps

As the documentation explains, you can install the Snyk CLI by running the npm package installation command:

npm install -g snyk
# OR
# yarn global add snyk

After installation, authenticate with Snyk:

snyk auth

This will open your browser to complete the authentication process.

Configuring Claude Desktop

To connect the Snyk MCP Server to Claude Desktop, you'll need to edit your claude_desktop_config.json file. 

• On macOS at ~/Library/Application Support/Claude/claude_desktop_config.json, 

• On Windows at %APPDATA%\Claude\claude_desktop_config.json

• On Ubuntu at /home/(your-username)/.config/Claude/claude_desktop_config.json

Add the following configuration to your claude_desktop_config.json:

{
  "mcpServers": {
    "snyk": {
      "command": "snyk",
      "args": [
        "mcp",
        "-t",
        "stdio"
      ],
      "env": {
        "SNYK_CFG_ORG": "your-org-id-here"
      }
    }
  }
}

Configuration notes:

• The SNYK_CFG_ORG environment variable is optional but recommended for setting a default organization

• You can set CLI environment variables for the MCP server either in the MCP server configuration file or directly on your system

• If you don't specify an organization ID, Snyk will use your default organization from your account settings

After saving the configuration file, restart Claude Desktop for the changes to take effect.

Available Snyk MCP tools

At the time of writing, the Snyk MCP Server already provides 11 security scanning tools that Claude can use to help secure your code:

Using Claude Desktop to patch vulnerabilities

For this demonstration, I've cloned the pyGoat repository from OWASP Project Leader adeyosemanputra. This project intentionally includes well-documented vulnerabilities (for educational purposes).

Scanning your codebase

With the Snyk MCP Server configured, you can simply ask Claude to scan your project:

User: Please run a code scan: /home/owler/Documents/Snyk/snyk-mcp-demos/pygoat

Claude will use the snyk_auth_status tool to verify authentication, and it will run a tool to get your approval to ‘trust’ the path you are scanning.

Then, Claude will execute snyk_code_scan on your project directory. The response includes:

• Total number of issues found

• Severity breakdown (High, Medium, Low)

• Specific vulnerability details with file paths and line numbers

• Descriptions of each security issue

For the pyGoat repository, the scan revealed 102 code issues:

• 16 High-severity vulnerabilities

• 44 Medium severity vulnerabilities

• 42 Low-severity vulnerabilities

Key high-severity issues included SQL Injection, Code Injection, Command Injection, Path Traversal, XML External Entity (XXE) Injection, deserialization vulnerabilities, and hardcoded secrets.

AI for vulnerability patching

The real power comes when you ask Claude to fix specific vulnerabilities. For example, with a high-severity SQL Injection vulnerability:

User: There's a SQL Injection vulnerability at introduction/views.py, line 871. 
Can you fix this vulnerability and then re-scan to show that it is fixed?

Can you fix this vulnerability and then re-scan to show that it is fixed?

Claude will:

1. Examine the vulnerable code using the filesystem MCP read_file tool, to understand the context

2. Identify the root cause (in this case, unsanitized user input concatenated directly into SQL queries)

3. Apply the fix using parameterized queries:

# BEFORE (vulnerable):
sql_query = "SELECT * FROM introduction_sql_lab_table WHERE id='"+name+"'AND password='"+password+"'"
  user = sql_lab_table.objects.raw(sql_query)

# AFTER (secure):
sql_query = "SELECT * FROM introduction_sql_lab_table WHERE id=%s AND password=%s"
  user = sql_lab_table.objects.raw(sql_query, [name, password])

1. Verify the fix by running another Snyk scan, confirming that the vulnerability count has decreased from 102 to 101 issues, with the specific SQL injection no longer appearing in the results (i.e., no new vulnerabilities have been added, and the previously identified vulnerability has been removed).

Is this the new DevSecOps paradigm?

This integration demonstrates how security can be integrated into modern, AI-native development workflows. Rather than security being a separate, often delayed concern, vulnerability detection and remediation become part of the natural development conversation.

The combination of Claude Desktop's conversational interface with the Snyk MCP Server means that security issues can be wrangled via simple natural language interfaces:

• Identified through comprehensive scanning

• Understood with AI-assisted analysis

• Fixed with context-aware patches

• Verified through automated re-scanning

All of this happens within the same interface where developers are already working, reducing context switching and accelerating the feedback loop between discovering and fixing security issues.

What else can Snyk’s official MCP Server do?

As MCP adoption grows and more security tools develop MCP servers, we can envision standard AI assistants that not only patch vulnerabilities but also:

• Generate security tests to prevent regressions

• Update documentation to reflect security fixes

• Create tickets for manual review of complex issues

• Provide security training by explaining vulnerabilities and fixes

The modular nature of the MCP protocol means these capabilities can evolve independently while remaining interoperable with tools exposed by other servers. I wrote about several other cybersecurity-oriented MCP servers that are open source and available online, here!

AI Assistants excel at handling routine, well-understood fixes while humans focus on novel security challenges that require creative problem-solving.

Bypassing Snyk usage limits with the Secure Developer Program

If you're actively developing and securing your projects, you'll quickly discover that Snyk's Free plan has monthly test limits: 400 tests for Open Source scanning, 100 tests for Code analysis, 300 tests for Infrastructure as Code, and 100 tests for Container scanning. For developers working on multiple projects or frequently iterating on security fixes, these limits can become a bottleneck, especially when you're trying to implement the scan-fix-rescan workflow we demonstrated above.

But here's the good news: if you're building open source projects, you can bypass these limitations entirely.

Through Snyk's Secure Developer Program, open source maintainers receive full Snyk Enterprise licenses with no usage limits. That means unlimited scans across all Snyk products—no more worrying about hitting your monthly cap when you're in the middle of hardening your codebase.

What you get as a Secure Developer Program member:

• Unlimited enterprise-grade security scanning for all your open source projects

• Access to all Snyk features with no restrictions

• A professional Snyk security badge for your README

• Community support through Snyk's Discord server

• Dedicated assistance setting up Snyk in your CI/CD pipelines

And since open source projects are increasingly important for career development—recruiters regularly review GitHub profiles to assess candidates—having comprehensive security tooling demonstrates that you write production-ready code that follows industry best practices.

The application process is straightforward. In exchange for adding a link back to Snyk in your README and allowing them to display your project logo, you get the same enterprise security platform that Fortune 500 companies use to protect their code.

Ready to secure your projects without limits? Apply to the Secure Developer Program and start building a portfolio that showcases both your development skills and your security expertise.