MCP Workflows & Troubleshooting

Individual MCP servers are useful. Combining them into workflows is where the real power lives. This guide covers four battle-tested workflows, security best practices, and a comprehensive troubleshooting reference.

Workflow 1: Database-Driven Development

MCP servers used: PostgreSQL + GitHub

The "query, investigate, fix, ship" loop — all from Claude Code.

The Workflow

Step 1: Investigate with data

Connect to the analytics database. Show me users who signed up
in the last 7 days but never completed onboarding. What step
are they dropping off at?

Step 2: Find the code

Based on that data, it looks like step 3 (email verification)
has a 60% drop-off. Find the code that handles email verification
in our codebase and look for potential issues.

Step 3: Fix and ship

Fix the race condition in the email verification handler.
Write a test that reproduces the bug. Then create a PR with
a clear description of what we found and fixed.

1{
2  "mcpServers": {
3    "analytics": {
4      "command": "npx",
5      "args": ["-y", "@modelcontextprotocol/server-postgres"],
6      "env": {
7        "DATABASE_URL": "${ANALYTICS_DB_URL}"
8      }
9    }
10  }
11}

Workflow 2: Full-Stack Debugging

MCP servers used: Sentry + GitHub + Filesystem

The "error to fix" pipeline for production bugs.

The Workflow

Step 1: Identify the error

What are the top 5 unresolved Sentry errors from the last 24 hours?
Show frequency, affected users, and stack traces.

Step 2: Correlate with code

The TypeError in checkout.ts looks related to the payment refactor
from last week. Show me the recent commits that touched checkout
and payment files.

Step 3: Fix and verify

I see the issue — the optional chaining was removed in commit abc123.
Fix it, add a regression test, and create a PR that references
the Sentry issue.

Workflow 3: Research-to-Code Pipeline

MCP servers used: Fetch + Memory

For academic and data users building API integrations.

The Workflow

Step 1: Research an API

Fetch the GBIF API documentation at https://www.gbif.org/developer/summary.
I need to understand how to query occurrence records by species and
location. Save the key endpoints and auth patterns to memory.

Step 2: Build on prior knowledge (later session)

What do we know about the GBIF API from our earlier research?
Now implement a Python function that queries coral reef species
occurrences within a bounding box around Mo'orea.

Step 3: Iterate with context

The API is returning 400 errors. Fetch the error codes documentation
and update our memory with the common error patterns. Then fix the query.

Workflow 4: CI/CD Integration

MCP servers used: GitHub + Shell Commands

Debug failing CI without leaving the terminal.

The Workflow

Check the CI status on my current branch. If there are failures,
show me the failing test names and error messages.

Run just the failing test locally so we can see the full output.

Fix the test. Run the full suite to make sure nothing else broke.
Push when it's green.

MCP Security Best Practices

Security is the most important consideration when connecting AI to real systems.

The Threat Landscape

Security Principles

1. Principle of Least Privilege

1-- GOOD: Read-only database user
2CREATE ROLE mcp_readonly WITH LOGIN PASSWORD 'secure-password';
3GRANT SELECT ON ALL TABLES IN SCHEMA public TO mcp_readonly;
4 
5-- BAD: Using your admin connection string — NEVER do this

2. Environment Variables for Secrets

1{
2  "mcpServers": {
3    "database": {
4      "command": "npx",
5      "args": ["-y", "@bytebase/dbhub", "--dsn"],
6      "env": {
7        "DATABASE_URL": "${DB_READONLY_URL}"
8      }
9    }
10  }
11}

Set actual values in your shell profile (which is in .gitignore):

# In ~/.zshrc
export DB_READONLY_URL="postgresql://readonly:pass@localhost:5432/myapp"

3. Review Third-Party MCP Code

# Clone and read the source before trusting it
git clone https://github.com/some-author/some-mcp-server
# Review: What does it access? Does it phone home?
# Are tool descriptions honest? Does it request more permissions than needed?

4. Auditing and Monitoring

claude mcp list               # Check active servers
claude mcp get <server-name>  # Inspect tools and permissions
claude --mcp-debug            # Verbose MCP logging

Security Checklist

MCP Troubleshooting Guide

Problem: Server Won't Connect

This is the most common MCP issue. Follow these steps systematically:

Problem: Error -32000 "Connection Closed"

The most common runtime error — the transport lost the connection.

Problem: Server Loses Connection Mid-Session

1# Restart without restarting Claude Code
2claude mcp restart <server-name>
3 
4# Or restart all
5claude mcp restart

Quick Diagnostic Checklist

Performance & Cost Considerations

API Rate Limits

Context Window Costs

Every MCP tool call adds tokens to the conversation:

• Tool descriptions loaded at start: ~500-2,000 tokens per server
• Each tool call result: Variable (100-10,000+ tokens)

When NOT to Use an MCP

The MCP Ecosystem in 2026

Adoption

• 97M+ monthly SDK downloads across Python and TypeScript
• Backed by Anthropic, OpenAI, Google, and Microsoft
• Integrated into VS Code, Cursor, Windsurf, Replit, and most AI IDEs
• Governed by the Agentic AI Foundation (Linux Foundation)

Server Discovery

• GitHub MCP Registry — Official collection
• mcp.so — Community directory with search
• PulseMCP — Curated directory with stats
• Smithery.ai — 2,200+ servers, marketplace-style

Emerging Patterns

• Multi-agent MCP workflows — Multiple Claude instances sharing servers
• MCP gateways — Proxy layers adding auth, rate limiting, and caching
• Multimodal MCP — 2026 roadmap includes images, audio, video as resource types
• Policy-as-Code — OPA-style rules controlling what tools can be called

Essential Commands Reference

Next Steps

1. Pick one workflow from this page that matches a real problem
2. Set up the MCP servers needed for that workflow
3. Run through it end-to-end, noting friction
4. Share .mcp.json with your team
5. Review security — read-only credentials and environment variables

Related Topics:

• Essential MCP Servers → — Server installation reference
• Building Custom MCPs → — Create your own
• MCP Fundamentals → — Protocol deep-dive