MongoDB MCP Server connects AI agents to MongoDB databases and MongoDB Atlas clusters through the Model Context Protocol. It lets agents interact with self-managed MongoDB deployments locally or use the hosted Atlas MCP server through the official plugins. The catalogue entries provide agent integrations and guidance for using the server.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add instructions/mongodb-js/mongodb-mcp-server/copilot-instructionsgit clone --depth 1 https://github.com/mongodb-js/mongodb-mcp-serverWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/instructions/mongodb-js/mongodb-mcp-server/copilot-instructions)<a href="https://agentmods.dev/instructions/mongodb-js/mongodb-mcp-server/copilot-instructions"><img src="https://agentmods.dev/badge/instructions/mongodb-js/mongodb-mcp-server/copilot-instructions.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.01576 | $0.01576 |
| Opus 5 | $0.00788 | $0.00788 |
| Sonnet 5 | $0.00315 | $0.00315 |
| Haiku 4.5 | $0.00158 | $0.00158 |
Grade A, and why
mongodb-mcp-server copilot-instructions.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 4d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 95 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Project Overview
This project is a monorepo implementing the MCP (Model Context Protocol) server that lets users interact with their MongoDB clusters and MongoDB Atlas accounts. It is built using TypeScript, Node.js, pnpm workspaces, and the official @modelcontextprotocol v2 SDK packages (client, server, core, node).
The server ships as the v3 API: a set of scoped @mongodb-js/mcp-* packages. The mongodb-mcp-server package is the binary CLI distribution (npx mongodb-mcp-server / MCPB) — library embedding uses the scoped packages.
Folder Structure
This project uses pnpm workspaces (pnpm-workspace.yaml). The source of the server lives in packages/*:
packages/mongodb-mcp-server: The shipped CLI binary entrypoint and its scripts.packages/cli: CLI wiring —runMcpCli,CliServer,Session,parseUserConfig,UserConfigSchema,applyConfigOverrides,create*FromConfigfactories,Resources.packages/core: Shared infrastructure —ToolBase/ToolClass,StdioRunner,InMemoryTransport,SessionStore,Keychain,Elicitation,NoopLogger,NoopTelemetry,McpServerre-export.packages/http-runners: HTTP transport —StreamableHttpRunner,MCPHttpServer,MonitoringServer.packages/tools-mongodb: MongoDB tools (MongoDBTools,MongoDBToolBase), connection management (MCPConnectionStore,MCPConnectionManager,ConnectionRegistry),ErrorCodes,MongoDBError.packages/tools-atlas: Atlas Admin API tools (AtlasTools).packages/tools-atlas-local: Atlas Local tools (AtlasLocalTools).packages/tools-assistant: Assistant / knowledge tools (AssistantTools).packages/atlas-api-client: Atlas API client (ApiClient,ClientCredentialsAuthProvider).packages/atlas-telemetry: Telemetry pipeline (AtlasTelemetry).packages/logging: Loggers (ConsoleLogger,DiskLogger,McpLogger).packages/metrics: Metrics (PrometheusMetrics,createDefaultMetrics).packages/types: Shared types (UserConfig,TransportRequestContext,ToolCategory,OperationType,ServerMetadata,McpSession, …).packages/ui: MCP UI resources (UIRegistry).- Test packages:
packages/integration-tests(start the server and interact with it),packages/accuracy-tests(accuracy tests that use different models to ensure tools have reliable descriptions),packages/eval-tests,packages/browser-tests,packages/test-utils. packages/scripts: repo maintenance scripts (API report generation, tool argument/UI generation, release notes).
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 4d ago First seen · 95 lines · 1,576 tokens per session scan A 811f9b2384af
mongodb-mcp-server copilot-instructions.md is an instructions file published in the GitHub repository mongodb-js/mongodb-mcp-server (1,121 stars, last pushed today), licensed Apache-2.0. It adds 1,576 tokens to every session, about $0.0079 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
Other instructions, from other repositories
vector-mcp AGENTS.md
Instructions for Knuckles-Team/vector-mcp, covering agents.md, scope, current architecture, non-negotiable design rules and source layout.
mongodb-mcp AGENTS.md
AGENTS.md instructions for VitalyOstanin/mongodb-mcp, covering repository guidelines, contributor notes, planning workflow, documentation guidelines and language policy.
mcp-database CLAUDE.md
Claude Code instructions for DiegoBulhoes/mcp-database, covering claude.md, commands, architecture, invariants (do not weaken) and adding or changing a tool.
vector-mcp CLAUDE.md
Instructions for Knuckles-Team/vector-mcp: Guidance for Claude Code (claude.ai/code) when working in this repository.
travel-mcp-server CLAUDE.md
Claude Code instructions for tanayshah11/travel-mcp-server, covering claude.md, project overview, commands, install (editable mode) and start mongodb (required).
mongodb-mcp CLAUDE.md
Claude Code instructions for VitalyOstanin/mongodb-mcp, covering instructions for claude code, location of agent instructions, what to do when working with instructions and file purposes.