cognee-mcp

cognee‑mcp - Run cognee’s memory engine as a Model Context Protocol server

Build memory for Agents and query from any client that speaks MCP – in your terminal or IDE.

✨ Features

• Multiple transports – choose Streamable HTTP --transport http (recommended for web deployments), SSE --transport sse (real‑time streaming), or stdio (classic pipe, default)

• Cloud Mode – connect to Cognee Cloud via --serve-url or COGNEE_SERVICE_URL env var (see Connection Modes)

• API Mode – connect to an already running Cognee FastAPI server (see Connection Modes)

• Minimal Memory API – exposes only remember, recall, and forget for agent memory workflows

• Integrated logging – all actions written to a rotating file (see get_log_file_location()) and mirrored to console in dev

• Session-aware memory – store fast session cache entries or permanent graph memory through one remember tool

• Focused recall – query memory through one recall tool with optional session and search controls

• Code graph search – inspect indexed symbols, dependencies, architecture, and change impact with code_search

• Simple deletion – remove a dataset or all owned memory through one forget tool

Please refer to our documentation here for further information.

Code graph search

Use code_search for deterministic queries against an indexed code dataset. Select an operation and pass its operation-specific filters in arguments:

{
  "operation": "query_facts",
  "arguments": {"kinds": ["module", "symbol"], "limit": 100},
  "datasets": "sample-code-dataset"
}

Supported operations are query_facts, explore, traverse, find_path, impact_analysis, insights, architecture and delta, plus the navigation operations capabilities, search, neighbors, subgraph, flows, hubs and ask. search and ask take a question in plain words as query.

Related MCP server: remembrallmcp

🚀 Quick Start

1. Clone cognee repo

   git clone https://github.com/topoteretes/cognee.git

2. Navigate to cognee-mcp subdirectory

   cd cognee/cognee-mcp

3. Install uv if you don't have one

   pip install uv

4. Install all the dependencies you need for cognee mcp server with uv

   uv sync --dev --all-extras --reinstall

5. Activate the virtual environment in cognee mcp directory

   source .venv/bin/activate

6. Set up your OpenAI API key in .env for a quick setup with the default cognee configurations

   LLM_API_KEY="YOUR_OPENAI_API_KEY"

7. Run cognee mcp server with stdio (default)

   python src/server.py

   or stream responses over SSE

   python src/server.py --transport sse

   or run with Streamable HTTP transport (recommended for web deployments)

   python src/server.py --transport http --host 127.0.0.1 --port 8000 --path /mcp

You can do more advanced configurations by creating .env file using our template. To use different LLM providers / database configurations, and for more info check out our documentation.

No API key? If your MCP host grants the sampling capability, LLM_PROVIDER="mcp-sampling" delegates completions to the host's own model, so no LLM_API_KEY is needed (embeddings still need a provider). Host support varies — as of early 2026 Claude Code does not yet grant sampling (anthropics/claude-code#1785). See the "MCP sampling" section of the .env template.

🐳 Docker Usage

If you'd rather run cognee-mcp in a container, you have two options:

1. Build locally

   1. Make sure you are in /cognee root directory and have a fresh .env containing only your LLM_API_KEY (and your chosen settings).

   2. Remove any old image and rebuild:

      docker rmi cognee/cognee-mcp:main || true
      docker build --no-cache -f cognee-mcp/Dockerfile -t cognee/cognee-mcp:main .

   3. Run it:

      # For HTTP transport (recommended for web deployments)
      docker run -e TRANSPORT_MODE=http --env-file ./.env -p 8000:8000 --rm -it cognee/cognee-mcp:main
      # For SSE transport
      docker run -e TRANSPORT_MODE=sse --env-file ./.env -p 8000:8000 --rm -it cognee/cognee-mcp:main
      # For stdio transport (default)
      docker run -e TRANSPORT_MODE=stdio --env-file ./.env --rm -it cognee/cognee-mcp:main

      Installing optional dependencies at runtime:

      You can install optional dependencies when running the container by setting the EXTRAS environment variable:

      # Install a single optional dependency group at runtime
      docker run \
        -e TRANSPORT_MODE=http \
        -e EXTRAS=aws \
        --env-file ./.env \
        -p 8000:8000 \
        --rm -it cognee/cognee-mcp:main
      
      # Install multiple optional dependency groups at runtime (comma-separated)
      docker run \
        -e TRANSPORT_MODE=sse \
        -e EXTRAS=aws,postgres,neo4j \
        --env-file ./.env \
        -p 8000:8000 \
        --rm -it cognee/cognee-mcp:main

      Available optional dependency groups:

      • aws - S3 storage support

      • postgres / postgres-binary - PostgreSQL database support

      • neo4j - Neo4j graph database support

      • neptune - AWS Neptune support

      • turso - Turso vector/graph store support

      • scraping - Web scraping capabilities

      • langchain - LangChain integration

      • llama-index - LlamaIndex integration

      • anthropic - Anthropic models

      • groq - Groq models

      • mistral - Mistral models

      • ollama / huggingface - Local model support

      • docs - Document processing

      • tracing - OpenTelemetry tracing

      • redis - Redis support

      • And more (see pyproject.toml for full list)

2. Pull from Docker Hub (no build required):

   The image is published to Docker Hub on every push to main. If you have not cloned the repo, create the .env file the run commands expect first — it needs at least your LLM key:

   # Pull the prebuilt image
   docker pull cognee/cognee-mcp:main
   
   # Create a minimal .env in the current directory (no repo checkout required)
   echo 'LLM_API_KEY="YOUR_OPENAI_API_KEY"' > .env

   # With HTTP transport (recommended for web deployments)
   docker run -e TRANSPORT_MODE=http --env-file ./.env -p 8000:8000 --rm -it cognee/cognee-mcp:main
   # With SSE transport
   docker run -e TRANSPORT_MODE=sse --env-file ./.env -p 8000:8000 --rm -it cognee/cognee-mcp:main
   # With stdio transport (default)
   docker run -e TRANSPORT_MODE=stdio --env-file ./.env --rm -it cognee/cognee-mcp:main

   With runtime installation of optional dependencies:

   # Install optional dependencies from Docker Hub image
   docker run \
     -e TRANSPORT_MODE=http \
     -e EXTRAS=aws,postgres \
     --env-file ./.env \
     -p 8000:8000 \
     --rm -it cognee/cognee-mcp:main

Important: Docker vs Direct Usage

Docker uses environment variables, not command line arguments:

• ✅ Docker: -e TRANSPORT_MODE=http

• ❌ Docker: --transport http (won't work)

Direct Python usage uses command line arguments:

• ✅ Direct: python src/server.py --transport http

• ❌ Direct: -e TRANSPORT_MODE=http (won't work)

Docker API Mode

To connect the MCP Docker container to a Cognee API server running on your host machine:

Simple Usage (Automatic localhost handling):

# Start your Cognee API server on the host
python -m cognee.api.client

# Run MCP container in API mode - localhost is automatically converted!
docker run \
  -e TRANSPORT_MODE=sse \
  -e API_URL=http://localhost:8000 \
  -e API_TOKEN=your_auth_token \
  -p 8001:8000 \
  --rm -it cognee/cognee-mcp:main

Note: The container will automatically convert localhost to host.docker.internal on Mac/Windows/Docker Desktop. You'll see a message in the logs showing the conversion.

Explicit host.docker.internal (Mac/Windows):

# Or explicitly use host.docker.internal
docker run \
  -e TRANSPORT_MODE=sse \
  -e API_URL=http://host.docker.internal:8000 \
  -e API_TOKEN=your_auth_token \
  -p 8001:8000 \
  --rm -it cognee/cognee-mcp:main

On Linux (use host network or container IP):

# Option 1: Use host network (simplest)
docker run \
  --network host \
  -e TRANSPORT_MODE=sse \
  -e API_URL=http://localhost:8000 \
  -e API_TOKEN=your_auth_token \
  --rm -it cognee/cognee-mcp:main

# Option 2: Use host IP address
# First, get your host IP: ip addr show docker0
docker run \
  -e TRANSPORT_MODE=sse \
  -e API_URL=http://172.17.0.1:8000 \
  -e API_TOKEN=your_auth_token \
  -p 8001:8000 \
  --rm -it cognee/cognee-mcp:main

Environment variables for API mode:

• API_URL: URL of the running Cognee API server

• API_TOKEN: Authentication token (optional, required if API has authentication enabled)

Note: When running in API mode:

• Database migrations are automatically skipped (API server handles its own DB)

• Some features are limited (see API Mode Limitations)

🔗 MCP Client Configuration

After starting your Cognee MCP server with Docker, you need to configure your MCP client to connect to it.

⚠️ Host/Origin protection (why you might get HTTP 421 or 403)

Both the http and sse transports validate the Host and Origin headers to block DNS-rebinding attacks, on every bind address including loopback — rebinding targets loopback services specifically, so 127.0.0.1 is not a mitigation.

• A Host the server does not recognise returns 421 Misdirected Request

• An Origin it does not recognise returns 403 Forbidden

When you bind a non-loopback address (--host 0.0.0.0, which is what the Docker entrypoint does), only localhost / 127.0.0.1 / [::1] are accepted by default, so reaching the server by LAN IP or a custom hostname returns 421 — the guard working, not a bug.

Allow specific hosts (the :* port glob is required):

-e MCP_ALLOWED_HOSTS="192.168.1.50:*,myserver.local:*"

Or turn the guard off entirely (only on a trusted network):

-e MCP_DISABLE_DNS_REBINDING_PROTECTION=true

Implementation note. FastMCP installs this guard on its streamable-http app only — create_sse_app() accepts no such option, so the allow-lists were silently dropped for SSE. cognee-mcp mounts the same middleware on the SSE app itself, with the same allow-lists, so both transports behave identically.

SSE Transport Configuration (Legacy — prefer HTTP below; both are guarded)

Start the server with SSE transport:

docker run -e TRANSPORT_MODE=sse --env-file ./.env -p 8000:8000 --rm -it cognee/cognee-mcp:main

Configure your MCP client:

Claude CLI (Easiest)

claude mcp add cognee-sse -t sse http://localhost:8000/sse

Verify the connection:

claude mcp list

You should see your server connected:

Checking MCP server health...

cognee-sse: http://localhost:8000/sse (SSE) - ✓ Connected

Manual Configuration

Claude (~/.claude.json)

{
  "mcpServers": {
    "cognee": {
      "type": "sse",
      "url": "http://localhost:8000/sse"
    }
  }
}

Cursor (~/.cursor/mcp.json)

{
  "mcpServers": {
    "cognee-sse": {
      "url": "http://localhost:8000/sse"
    }
  }
}

HTTP Transport Configuration (Recommended)

Start the server with HTTP transport:

docker run -e TRANSPORT_MODE=http --env-file ./.env -p 8000:8000 --rm -it cognee/cognee-mcp:main

Configure your MCP client:

Claude CLI (Easiest)

claude mcp add cognee-http -t http http://localhost:8000/mcp

Verify the connection:

claude mcp list

You should see your server connected:

Checking MCP server health...

cognee-http: http://localhost:8000/mcp (HTTP) - ✓ Connected

Manual Configuration

Claude (~/.claude.json)

{
  "mcpServers": {
    "cognee": {
      "type": "http",
      "url": "http://localhost:8000/mcp"
    }
  }
}

Cursor (~/.cursor/mcp.json)

{
  "mcpServers": {
    "cognee-http": {
      "url": "http://localhost:8000/mcp"
    }
  }
}

Dual Configuration Example

You can configure both transports simultaneously for testing:

{
  "mcpServers": {
    "cognee-sse": {
      "type": "sse",
      "url": "http://localhost:8000/sse"
    },
    "cognee-http": {
      "type": "http",
      "url": "http://localhost:8000/mcp"
    }
  }
}

Note: Only enable the server you're actually running to avoid connection errors.

🌐 Connection Modes

The MCP server supports three connection modes:

Direct Mode (Default)

The MCP server directly imports and uses the cognee library with local databases (SQLite, LanceDB, Ladybug). This is the default mode with full feature support.

Cloud Mode

Connect to Cognee Cloud or a remote Cognee instance. The server calls cognee.serve() at startup, and all SDK operations transparently route to the cloud. No local databases needed.

Via CLI flags:

python src/server.py --serve-url https://your-instance.cognee.ai --serve-api-key ck_...

Via environment variables (zero-config):

export COGNEE_SERVICE_URL="https://your-instance.cognee.ai"
export COGNEE_API_KEY="ck_..."
python src/server.py

Cloud Mode with Docker:

docker run \
  -e TRANSPORT_MODE=sse \
  -e COGNEE_SERVICE_URL=https://your-instance.cognee.ai \
  -e COGNEE_API_KEY=ck_... \
  -p 8000:8000 \
  --rm -it cognee/cognee-mcp:main

Cloud Mode arguments / environment variables:

• --serve-url / COGNEE_SERVICE_URL: Cognee Cloud or remote instance URL

• --serve-api-key / COGNEE_API_KEY: API key for the instance

Database migrations are automatically skipped in Cloud mode.

API Mode

The MCP server connects to an already running Cognee FastAPI server via HTTP requests. This is useful when:

• You have a centralized Cognee API server running

• You want to separate the MCP server from the knowledge graph backend

• You need multiple MCP servers to share the same knowledge graph

Starting the MCP server in API mode:

# Start your Cognee FastAPI server first (default port 8000)
cd /path/to/cognee
python -m cognee.api.client

# Then start the MCP server in API mode
cd cognee-mcp
python src/server.py --api-url http://localhost:8000 --api-token YOUR_AUTH_TOKEN

API Mode with different transports:

# With SSE transport
python src/server.py --transport sse --api-url http://localhost:8000 --api-token YOUR_TOKEN

# With HTTP transport
python src/server.py --transport http --api-url http://localhost:8000 --api-token YOUR_TOKEN

API Mode with Docker:

# On Mac/Windows (use host.docker.internal to access host)
docker run \
  -e TRANSPORT_MODE=sse \
  -e API_URL=http://host.docker.internal:8000 \
  -e API_TOKEN=YOUR_TOKEN \
  -p 8001:8000 \
  --rm -it cognee/cognee-mcp:main

# On Linux (use host network)
docker run \
  --network host \
  -e TRANSPORT_MODE=sse \
  -e API_URL=http://localhost:8000 \
  -e API_TOKEN=YOUR_TOKEN \
  --rm -it cognee/cognee-mcp:main

Command-line arguments for API mode:

• --api-url: Base URL of the running Cognee FastAPI server (e.g., http://localhost:8000)

• --api-token: Authentication token for the API (optional, required if API has authentication enabled)

Docker environment variables for API mode:

• API_URL: Base URL of the running Cognee FastAPI server

• API_TOKEN: Authentication token (optional, required if API has authentication enabled)

API Mode behavior: The MCP server intentionally exposes only the memory API: remember, recall, and forget (plus the cognify_status progress check). In API mode these tools call the Cognee API server endpoints directly. Operational helpers such as cognify, search, list_data, delete, prune, improve, and document retrieval helpers are kept internal and are not exposed as MCP tools.

💻 Basic Usage

The MCP server exposes its functionality through tools. Call them from any MCP client (Cursor, Claude Desktop, Cline, Roo and more).

Available Tools

The MCP server exposes four tools (three memory tools pinned in tools/list, plus cognify_status):

• remember: Store data in memory. Pass data for text, or filename + content_base64 to ingest an uploaded file (up to 10 MB). With session_id: fast session cache (text only). Without session_id: permanent graph memory

• recall: Search memory with auto-routing. Searches session cache first when session_id is provided, then falls through to the permanent graph

• forget: Delete memory by dataset name or id, a single data item by data_id, or delete all owned memory with everything=True

• cognify_status: Check the progress of background ingestion started by remember(background=True). Unadvertised by default; discoverable via search_tools and callable by name

Recall result summaries

recall (the MCP memory-search tool) starts every successful response with a summary, followed by the same result body as before:

3 memories found (2 from sessions, 1 from project docs)
[session] ...

The count is the number of returned memory entries, not top_k, underlying chunks used to synthesize an answer, or system status messages. Source and dataset hints use metadata already present in the returned entries; no recency lookup or extra LLM call is made.

Empty results distinguish an empty memory graph, indexing in progress, indexing failure, and no match. When available, progress is displayed as, for example, still indexing — 12/40 items processed, retry shortly. These are data items, not an inferred chunk count. A graph with no recorded indexing run is reported as not yet indexed. If the status check fails or exceeds its two-second budget, the summary explicitly says memory status is unavailable. Successful hits do not trigger status checks.

The MCP content remains a single TextContent block. Text consumers can separate line one from the unchanged body with text.partition("\n"). Machine consumers can read content[0]._meta["cognee/memory"], containing count and state.

state is one of four values, one per action a caller can take:

indexing additionally carries completed/total when the pipeline reports them. Tool errors retain their existing Error: response.

Tool surface (COGNEE_MCP_TOOL_MODE)

Advertising every tool up front costs agent context and hurts tool-selection accuracy, so by default the server pins a small set in tools/list and makes the rest discoverable through FastMCP's built-in search_tools. Unadvertised tools stay callable by name.

COGNEE_MCP_TOOL_MODE=default   # pinned: remember, recall, forget
COGNEE_MCP_TOOL_MODE=minimal   # pinned: remember, recall, forget
COGNEE_MCP_TOOL_MODE=all       # no search transform; advertise every tool

Also settable per-process with --tool-mode. In default/minimal an agent calls search_tools(query=...) to find a tool and either calls it by name or goes through the call_tool proxy. Tiers are declared per tool via @registry.tool(tags={...}) in src/server.py, so the pinned set is derived from the decorators rather than a separate list.

search_tools returns up to TOOL_SEARCH_MAX_RESULTS (10) tools, sized for a catalog that will grow. The window only costs context on turns that actually call search; tools/list stays constant either way. See tests/test_tool_search_benchmark.py for the recall sweep behind the number.

Writing a tool so search can find it

Search works well on natural-language queries. Every phrasing below returns its target ranked first (covered by tests/test_tool_search.py):

The one thing to know when adding a tool: matching is purely lexical. FastMCP's BM25 tokenizer does no stemming and drops tools that score zero, so a query shares no credit with a word it doesn't literally contain. Multi-word queries paper over this (they usually contain some matching token), which is why the table above passes, but terse queries won't.

So: write descriptions in the words an agent would use, including both singular and plural. Recall is bounded by vocabulary, not by TOOL_SEARCH_MAX_RESULTS. If lexical matching ever stops being enough, BaseSearchTransform leaves _search() abstract — a semantic ranker over cognee's own embeddings can be dropped in without touching the rest of the plumbing.

Agent Scoping (per-client default datasets)

By default, each MCP client gets its own auto-named dataset (e.g. Cursor → cursor_vscode_memory, Claude Code → claude_code_memory) so different agents don't share memory unintentionally. The dataset is created on demand the first time a client writes to it.

remember and cognify_status route to the agent-scoped dataset when dataset_name is omitted (the internal cognify/improve helpers, which are not exposed as tools, do the same). Pass dataset_name explicitly to override (e.g. dataset_name="main_dataset" still works).

To disable agent scoping and have all clients share main_dataset as the default, set in .env:

COGNEE_MCP_AGENT_SCOPED=false

When disabled, no per-client datasets are autocreated.

Per-dataset isolation (ENABLE_BACKEND_ACCESS_CONTROL)

Agent scoping decides which dataset name a tool defaults to. Whether two datasets are actually isolated at the storage layer is governed by cognee's ENABLE_BACKEND_ACCESS_CONTROL flag:

• true (default) — each (user, dataset) pair gets its own per-dataset Kuzu + LanceDB under .cognee_system/databases/<dataset_uuid>/, and search is strictly per-dataset.

• false — all datasets share one Kuzu graph DB and one LanceDB. The dataset filter is honored for top-level data points, but GRAPH_COMPLETION traversal can pull connected nodes from any dataset. Use for single-user local dev; also disables the API auth requirement unless REQUIRE_AUTHENTICATION=true is set explicitly.

Switching modes wipes nothing automatically — but data does not migrate. Data ingested in one mode lives at a different on-disk path than the other and won't be visible after the flip. Clean-slate when changing the flag:

# Stop server, then:
DATA_ROOT="/absolute/path/to/data-root"
rm -rf "$DATA_ROOT/.cognee_system" "$DATA_ROOT/.data_storage"
# Edit .env to flip ENABLE_BACKEND_ACCESS_CONTROL, restart, re-cognify.

(Set DATA_ROOT to whatever you used for DATA_ROOT_DIRECTORY / SYSTEM_ROOT_DIRECTORY, or your cognee install dir if you didn't set those.)

Examples:

# Store permanent memory
remember(data="Cognee MCP now exposes a focused memory API.", dataset_name="main_dataset")

# Store permanent memory without the automatic improve stage (add + cognify still run)
remember(data="A new fact", dataset_name="main_dataset", self_improvement=False)

# The opt-out also applies to file uploads and background=True ingestion
remember(data="A new fact", self_improvement=False, background=True)

# Store session memory without a background graph bridge in direct mode
remember(data="Temporary working note", session_id="agent-session-1", self_improvement=False)

# Recall from memory
recall(query="What changed in the MCP server?", session_id="agent-session-1")

# Delete one dataset
forget(dataset="main_dataset")

self_improvement defaults to True; only an explicit False is forwarded, so True leaves the core default in charge. In permanent mode, False disables automatic improvement without skipping ingestion or graph building. In direct session mode, it disables the automatic session-to-graph bridge while still storing the session entry. In API session mode, MCP uses typed QA entries, which stay in the session cache for all flag values; the flag does not enable a graph bridge there. It does not control separately requested skill improvement.

Select an uploaded ontology for a write

Pass ontology_key to remember to ground permanent-memory extraction with one or more previously uploaded OWL ontologies:

remember(data="Alice works at Acme.", dataset_name="workspace_a", ontology_key="workspace_a_v2")
remember(
    data="Acme develops software.",
    ontology_key=["organizations", "software"],
    background=True,
)

In API mode, upload the ontologies first through POST /api/v1/ontologies using the same authenticated user as the MCP server. Keys are sent as repeated ontology_key form fields. In local mode, keys resolve through OntologyService in the default user's local ontology store; remote uploads are not copied locally. Unknown or inaccessible keys fail the write. Background failures are reported by cognify_status.

Omitting ontology_key (or passing an empty list) preserves the configured server ontology, including ONTOLOGY_FILE_PATH. Ontology selection is only for permanent writes: combining a nonempty key with session_id returns an error because session-cache writes do not perform extraction.

Development and Debugging

Debugging

Use the fastmcp CLI, not mcp. Since the FastMCP 3 migration this server is a standalone fastmcp.FastMCP instance, which the mcp CLI does not recognise — mcp dev src/server.py fails with "Ignoring object 'src/server.py:mcp' as it's not a valid server object".

Inspect the server without launching anything (fast sanity check — name, version, tool count):

uv run fastmcp inspect src/server.py:mcp

Run it against the MCP Inspector UI:

uv run fastmcp dev src/server.py:mcp

Open the inspector with a longer timeout — cognee's first call can be slow while the databases initialise:

http://localhost:5173?timeout=120000

To apply new changes while developing cognee:

1. Update dependencies in the cognee folder if needed

2. uv sync --group dev --reinstall

3. uv run fastmcp dev src/server.py:mcp

The :mcp suffix names the server object in the file. Without it the CLI has to guess, and the guess is not reliable across FastMCP versions.

Development

In order to use local cognee:

1. Uncomment the following line in the cognee-mcp pyproject.toml file and set the cognee root path.

   #"cognee[postgres-binary,docs,neo4j] @ file:/path/to/your/cognee"

   Replace /path/to/your/cognee with the absolute path to your cognee checkout, and comment out the released "cognee[...]>=1.5.0,<2.0.0" line directly below it — otherwise both requirements apply and uv resolves the published package instead.

2. Install dependencies with uv in the mcp folder

   uv sync --reinstall

   Re-run this after every change to the local cognee checkout.

Note: editing that line modifies the tracked pyproject.toml and rewrites uv.lock with a machine-local absolute path. Revert both before committing — git checkout -- pyproject.toml uv.lock — or the path leaks into the repo.

Code of Conduct

We are committed to making open source an enjoyable and respectful experience for our community. See CODE_OF_CONDUCT for more information.

💫 Contributors

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