[BUG] MCP Tools Not Available to Claude Assistant Despite Being Loaded Successfully

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

MCP Tools Not Available to Claude Assistant Despite Being Loaded Successfully

Summary

MCP server tools are successfully loaded and visible in Cursor's MCP settings UI, but are not accessible to the Claude Code assistant for invocation. The MCP server logs show all tools are loaded correctly (42 tools for n8n-sandbox-mcp), but when attempting to invoke them, Claude reports "No such tool available".

Environment

• IDE: Cursor
• Extension: Claude Code (latest)
• OS: macOS (Darwin 25.1.0)
• MCP Server: n8n-mcp (latest from npm)
• MCP Config Location: ~/.cursor/mcp.json

Actual Behavior

• Cursor's MCP UI shows all 42 tools from n8n-sandbox-mcp server
• Server logs confirm: "Found 42 tools, 0 prompts, and 0 resources"
• Claude assistant can only access 23 tools (documentation/validation tools)
• Claude assistant cannot access the 19 n8n API management tools (n8n_list_workflows, n8n_create_workflow, etc.)
• Attempting to invoke unavailable tools returns: Error: No such tool available: mcp__n8n-sandbox-mcp__n8n_health_check

Analysis

The issue appears to be in how the Claude Code extension bridges MCP server capabilities to the Claude assistant:

1. ✅ MCP server loads correctly (stdio transport)
2. ✅ Environment variables are passed successfully
3. ✅ Cursor's MCP layer can discover all tools
4. ✅ Tools appear in Cursor's settings UI
5. ❌ Tools are NOT exposed to Claude Code assistant for invocation

This suggests a disconnect between:

• Cursor's MCP discovery/UI layer (working)
• Claude Code assistant's tool invocation layer (not working for all tools)

Possible Causes

1. Tool filtering: Claude Code extension may be filtering or limiting which tools are exposed to the assistant
2. Tool naming convention: Tools with certain prefixes (like n8n_*) might not be properly passed through
3. Dynamic tool loading: Tools that require API configuration (env vars) might not be registered correctly
4. MCP protocol version mismatch: Different interpretation of MCP protocol between server and client

Workaround

Users can interact with n8n API directly via HTTP requests instead of using the MCP tools, but this defeats the purpose of having an MCP integration.

Impact

• MCP servers with optional features (enabled via environment variables) cannot be fully utilized
• Users see tools in UI but cannot use them, creating confusion
• Limits the usefulness of the MCP ecosystem in Claude Code

Additional Context

• This issue is specific to tools that are conditionally loaded based on environment variables
• Base tools (always available) work correctly
• The same MCP server works correctly when tested standalone
• Issue persists across Cursor restarts

---

Related: This may affect other MCP servers that provide different tool sets based on configuration/authentication.

What Should Happen?

Expected Behavior

When an MCP server is configured and successfully loads tools (as shown in Cursor's MCP settings and server logs), those tools should be available for the Claude Code assistant to invoke via the MCP protocol.

Error Messages/Logs

## Evidence

### MCP Server Logs (Successful)

2025-11-07 13:00:33.244 [info] Successfully connected to stdio server
2025-11-07 13:00:33.244 [info] Storing stdio client project-0-projects-n8n-sandbox-mcp
2025-11-07 13:01:04.295 [info] Handling ListOfferings action, server stored: true
2025-11-07 13:01:04.295 [info] Connected to stdio server, fetching offerings
2025-11-07 13:01:04.308 [info] Found 42 tools, 0 prompts, and 0 resources


### Manual Server Test (Successful)
When running the n8n-mcp server manually with environment variables:

export N8N_API_URL="your-url"
export N8N_API_KEY="your-key"
npx -y n8n-mcp


Output:

[INFO] MCP server initialized with 42 tools (n8n API: configured)


Without environment variables:

[INFO] MCP server initialized with 23 tools (n8n API: not configured)


### Tools Visible in Cursor UI
Cursor's MCP settings show all tools including:
- `n8n_list_workflows`
- `n8n_create_workflow`
- `n8n_get_workflow`
- `n8n_update_partial_workflow`
- `n8n_health_check`
- And 14+ more n8n API tools

### Claude Assistant Available Tools
Only these n8n-mcp tools are accessible to Claude:
- `search_nodes`
- `list_nodes`
- `get_node_info`
- `validate_workflow`
- `search_templates`
- And ~18 other documentation/validation tools

Missing from Claude's available tools (but visible in Cursor UI):
- All `n8n_*` prefixed tools (19 tools)

Steps to Reproduce

Steps to Reproduce

1. Install n8n-mcp server via npm:

``bash
npx -y n8n-mcp
``

1. Configure MCP server in ~/.cursor/mcp.json:

``json
{
"mcpServers": {
"n8n-sandbox-mcp": {
"command": "npx",
"args": ["-y", "n8n-mcp"],
"env": {
"MCP_MODE": "stdio",
"LOG_LEVEL": "info",
"DISABLE_CONSOLE_OUTPUT": "false",
"N8N_API_URL": "https://your-n8n-instance.com/",
"N8N_API_KEY": "your-api-key"
}
}
}
}
``

1. Restart Cursor

1. Verify in Cursor Settings → Tools & MCP:

• Server shows as enabled
• All 42 tools are listed (including n8n_list_workflows, n8n_create_workflow, etc.)

1. Check MCP server output logs (View → Output → MCP: n8n-sandbox-mcp):

``
[info] Successfully connected to stdio server
[info] Found 42 tools, 0 prompts, and 0 resources
``

1. Ask Claude Code assistant to check available tools or invoke an n8n API tool:

``
Try to invoke: mcp__n8n-sandbox-mcp__n8n_health_check
``

1. Observe error: No such tool available

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

v2.0.35

Platform

Google Vertex AI

Operating System

macOS

Terminal/Shell

Cursor

Additional Information

_No response_