Claude Code vs. Cursor: Which AI Coding Agent Should You Use in 2026?

Claude Code and Cursor both support MCP, both run background agents, and both can connect to GitHub, Vercel, Slack, and more. The real difference is workflow philosophy.

Claude Code and Cursor both support MCP tool calls. Both can connect to GitHub, Vercel, Slack, Notion, and dozens of other services. Both run autonomous background agents. The difference isn't capability — it's workflow philosophy. And which one you choose changes how you should configure your service permissions.

The Core Difference

Claude Code

Agent-first

Lives in the terminal. You give it a goal — "refactor the auth module and open a PR" — and it works autonomously. Best for long-running, multi-step tasks where you want the agent running in the background while you do something else.

Cursor

IDE-first

Lives in your editor. The AI is deeply integrated into your coding environment — inline completions, file-aware chat, multi-file edits. Best for active coding sessions where you want AI assistance at your fingertips.

MCP Support: How Each One Connects

Both tools use MCP for external service connections, but the configuration is different:

Claude Desktop / Claude Code

OAuth-based MCP connection

You connect by visiting the Stow base URL in a browser and completing an OAuth flow. Claude Desktop stores the connection. Each time Claude makes a tool call, it goes through the authenticated connection.

The OAuth flow means the agent never has the raw token — the authentication is session-based.

Cursor

SSE JSON config in mcp_config.json

You paste a JSON configuration block with the Stow SSE endpoint URL plus your agent_id and agent_secret. Cursor sends these credentials with each MCP request.

The agent_secret is a Stow-specific credential — it identifies your agent to the Stow permission layer, not the underlying service token.

Permission Implications

The agent-first vs. IDE-first distinction matters for how you configure permissions.

Claude Code agent sessions

Claude Code often runs long multi-step tasks with multiple tool calls in sequence. Permissions need to account for the full workflow: if the task is "refactor and PR," Claude needs GitHub read and write access for that session.

Consider: session-scoped Security Baselines that grant slightly broader read access for autonomous tasks, with write operations as Approval Required.

Cursor interactive sessions

Cursor is used interactively — you're present when it makes tool calls. Permissions can be slightly tighter since you'll see the call happening and can intervene before it completes.

Consider: narrower baseline permissions with Approval Required for writes, since you're available to approve in real time.

Feature Comparison

Feature	Claude Code	Cursor
Primary interface	Terminal / CLI	Code editor (VS Code-based)
Agent mode	Background autonomous	Interactive + background
MCP support	Yes (OAuth)	Yes (SSE JSON)
Inline code completion	No	Yes
Multi-file context	Yes	Yes
Long-running tasks	Excellent	Good
Codebase indexing	Session-based	Persistent index
Stow integration	Yes (Claude Desktop OAuth)	Yes (SSE config)
Pricing model	API usage / Claude Pro	Subscription tiers

The Recommended Setup: Run Both

The most common pattern for experienced teams is using both — Cursor for active coding sessions and Claude Code for longer autonomous tasks. With Stow, you can configure separate Security Baselines for each agent, so their permissions don't overlap.

Dual-agent setup with Stow

Cursor agent: GitHub read, Neon branch access, Vercel read — active dev tools only

Claude Code agent: GitHub read + PR creation, Slack post (approval required), Notion write — broader comms + output tools

Each agent has its own agent_id and agent_secret in Stow. The activity log shows which agent made which call. If something unexpected happens, you can trace it to the specific agent and session.

Which One to Start With

Start with Cursor if you spend most of your day in a code editor and want inline AI assistance as your primary mode.
Start with Claude Code if you prefer terminal-based workflows and want to run autonomous multi-step tasks in the background.
Run both if you do active coding (Cursor) and background automation (Claude Code) and want separate permission scopes for each.

One Permission Layer. Every Agent.

Run Claude Code and Cursor through Stow with separate baselines, shared audit log, and unified control.

Stow Security Team

April 19, 2026