How to integrate Pinecone MCP with Autogen

This guide walks you through connecting Pinecone to AutoGen using the Composio tool router. By the end, you'll have a working Pinecone agent that can query all vectors similar to user question, upsert document embeddings into a namespace, delete vectors from the archive index through natural language commands. This guide will help you understand how to give your AutoGen agent real control over a Pinecone account through Composio's Pinecone MCP server. Before we dive in, let's take a quick look at the key ideas and tools involved.

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Pinecone is a fully managed vector database for high-performance AI memory and search. It lets you scale semantic search and retrieval without infrastructure overhead.

30 Tools

Introduction

This guide walks you through connecting Pinecone to AutoGen using the Composio tool router. By the end, you'll have a working Pinecone agent that can query all vectors similar to user question, upsert document embeddings into a namespace, delete vectors from the archive index through natural language commands.

This guide will help you understand how to give your AutoGen agent real control over a Pinecone account through Composio's Pinecone MCP server.

Before we dive in, let's take a quick look at the key ideas and tools involved.

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TL;DR

Here's what you'll learn:
  • Get and set up your OpenAI and Composio API keys
  • Install the required dependencies for Autogen and Composio
  • Initialize Composio and create a Tool Router session for Pinecone
  • Wire that MCP URL into Autogen using McpWorkbench and StreamableHttpServerParams
  • Configure an Autogen AssistantAgent that can call Pinecone tools
  • Run a live chat loop where you ask the agent to perform Pinecone operations

What is AutoGen?

Autogen is a framework for building multi-agent conversational AI systems from Microsoft. It enables you to create agents that can collaborate, use tools, and maintain complex workflows.

Key features include:

  • Multi-Agent Systems: Build collaborative agent workflows
  • MCP Workbench: Native support for Model Context Protocol tools
  • Streaming HTTP: Connect to external services through streamable HTTP
  • AssistantAgent: Pre-built agent class for tool-using assistants

What is the Pinecone MCP server, and what's possible with it?

The Pinecone MCP server is an implementation of the Model Context Protocol that connects your AI agent and assistants like Claude, Cursor, etc directly to your Pinecone account. It provides structured and secure access so your agent can perform Pinecone operations on your behalf.

What is the Composio tool router, and how does it fit here?

What is Composio SDK?

Composio's Composio SDK helps agents find the right tools for a task at runtime. You can plug in multiple toolkits (like Gmail, HubSpot, and GitHub), and the agent will identify the relevant app and action to complete multi-step workflows. This can reduce token usage and improve the reliability of tool calls. Read more here: Getting started with Composio SDK

The tool router generates a secure MCP URL that your agents can access to perform actions.

How the Composio SDK works

The Composio SDK follows a three-phase workflow:

  1. Discovery: Searches for tools matching your task and returns relevant toolkits with their details.
  2. Authentication: Checks for active connections. If missing, creates an auth config and returns a connection URL via Auth Link.
  3. Execution: Executes the action using the authenticated connection.

Step-by-step Guide

Step by step08 STEPS
1

Prerequisites

You will need:

  • A Composio API key
  • An OpenAI API key (used by Autogen's OpenAIChatCompletionClient)
  • A Pinecone account you can connect to Composio
  • Some basic familiarity with Autogen and Python async
2

Getting API Keys for OpenAI and Composio

OpenAI API Key
  • Go to the OpenAI dashboard and create an API key. You'll need credits to use the models, or you can connect to another model provider.
  • Keep the API key safe.
Composio API Key
  • Log in to the Composio dashboard.
  • Navigate to your API settings and generate a new API key.
  • Store this key securely as you'll need it for authentication.
3

Install dependencies

bash
pip install composio python-dotenv
pip install autogen-agentchat autogen-ext-openai autogen-ext-tools

Install Composio, Autogen extensions, and dotenv.

What's happening:

  • composio connects your agent to Pinecone via MCP
  • autogen-agentchat provides the AssistantAgent class
  • autogen-ext-openai provides the OpenAI model client
  • autogen-ext-tools provides MCP workbench support

4

Set up environment variables

bash
COMPOSIO_API_KEY=your-composio-api-key
OPENAI_API_KEY=your-openai-api-key
USER_ID=your-user-identifier@example.com

Create a .env file in your project folder.

What's happening:

  • COMPOSIO_API_KEY is required to talk to Composio
  • OPENAI_API_KEY is used by Autogen's OpenAI client
  • USER_ID is how Composio identifies which user's Pinecone connections to use
5

Import dependencies and create Tool Router session

python
import asyncio
import os
from dotenv import load_dotenv
from composio import Composio

from autogen_agentchat.agents import AssistantAgent
from autogen_ext.models.openai import OpenAIChatCompletionClient
from autogen_ext.tools.mcp import McpWorkbench, StreamableHttpServerParams

load_dotenv()

async def main():
    # Initialize Composio and create a Pinecone session
    composio = Composio(api_key=os.getenv("COMPOSIO_API_KEY"))
    session = composio.create(
        user_id=os.getenv("USER_ID"),
        toolkits=["pinecone"]
    )
    url = session.mcp.url
What's happening:
  • load_dotenv() reads your .env file
  • Composio(api_key=...) initializes the SDK
  • create(...) creates a Tool Router session that exposes Pinecone tools
  • session.mcp.url is the MCP endpoint that Autogen will connect to
6

Configure MCP parameters for Autogen

python
# Configure MCP server parameters for Streamable HTTP
server_params = StreamableHttpServerParams(
    url=url,
    timeout=30.0,
    sse_read_timeout=300.0,
    terminate_on_close=True,
    headers={"x-api-key": os.getenv("COMPOSIO_API_KEY")}
)

Autogen expects parameters describing how to talk to the MCP server. That is what StreamableHttpServerParams is for.

What's happening:

  • url points to the Tool Router MCP endpoint from Composio
  • timeout is the HTTP timeout for requests
  • sse_read_timeout controls how long to wait when streaming responses
  • terminate_on_close=True cleans up the MCP server process when the workbench is closed
7

Create the model client and agent

python
# Create model client
model_client = OpenAIChatCompletionClient(
    model="gpt-5",
    api_key=os.getenv("OPENAI_API_KEY")
)

# Use McpWorkbench as context manager
async with McpWorkbench(server_params) as workbench:
    # Create Pinecone assistant agent with MCP tools
    agent = AssistantAgent(
        name="pinecone_assistant",
        description="An AI assistant that helps with Pinecone operations.",
        model_client=model_client,
        workbench=workbench,
        model_client_stream=True,
        max_tool_iterations=10
    )

What's happening:

  • OpenAIChatCompletionClient wraps the OpenAI model for Autogen
  • McpWorkbench connects the agent to the MCP tools
  • AssistantAgent is configured with the Pinecone tools from the workbench
8

Run the interactive chat loop

python
print("Chat started! Type 'exit' or 'quit' to end the conversation.\n")
print("Ask any Pinecone related question or task to the agent.\n")

# Conversation loop
while True:
    user_input = input("You: ").strip()

    if user_input.lower() in ["exit", "quit", "bye"]:
        print("\nGoodbye!")
        break

    if not user_input:
        continue

    print("\nAgent is thinking...\n")

    # Run the agent with streaming
    try:
        response_text = ""
        async for message in agent.run_stream(task=user_input):
            if hasattr(message, "content") and message.content:
                response_text = message.content

        # Print the final response
        if response_text:
            print(f"Agent: {response_text}\n")
        else:
            print("Agent: I encountered an issue processing your request.\n")

    except Exception as e:
        print(f"Agent: Sorry, I encountered an error: {str(e)}\n")
What's happening:
  • The script prompts you in a loop with You:
  • Autogen passes your input to the model, which decides which Pinecone tools to call via MCP
  • agent.run_stream(...) yields streaming messages as the agent thinks and calls tools
  • Typing exit, quit, or bye ends the loop

Complete Code

Here's the complete code to get you started with Pinecone and AutoGen:

python
import asyncio
import os
from dotenv import load_dotenv
from composio import Composio

from autogen_agentchat.agents import AssistantAgent
from autogen_ext.models.openai import OpenAIChatCompletionClient
from autogen_ext.tools.mcp import McpWorkbench, StreamableHttpServerParams

load_dotenv()

async def main():
    # Initialize Composio and create a Pinecone session
    composio = Composio(api_key=os.getenv("COMPOSIO_API_KEY"))
    session = composio.create(
        user_id=os.getenv("USER_ID"),
        toolkits=["pinecone"]
    )
    url = session.mcp.url

    # Configure MCP server parameters for Streamable HTTP
    server_params = StreamableHttpServerParams(
        url=url,
        timeout=30.0,
        sse_read_timeout=300.0,
        terminate_on_close=True,
        headers={"x-api-key": os.getenv("COMPOSIO_API_KEY")}
    )

    # Create model client
    model_client = OpenAIChatCompletionClient(
        model="gpt-5",
        api_key=os.getenv("OPENAI_API_KEY")
    )

    # Use McpWorkbench as context manager
    async with McpWorkbench(server_params) as workbench:
        # Create Pinecone assistant agent with MCP tools
        agent = AssistantAgent(
            name="pinecone_assistant",
            description="An AI assistant that helps with Pinecone operations.",
            model_client=model_client,
            workbench=workbench,
            model_client_stream=True,
            max_tool_iterations=10
        )

        print("Chat started! Type 'exit' or 'quit' to end the conversation.\n")
        print("Ask any Pinecone related question or task to the agent.\n")

        # Conversation loop
        while True:
            user_input = input("You: ").strip()

            if user_input.lower() in ['exit', 'quit', 'bye']:
                print("\nGoodbye!")
                break

            if not user_input:
                continue

            print("\nAgent is thinking...\n")

            # Run the agent with streaming
            try:
                response_text = ""
                async for message in agent.run_stream(task=user_input):
                    if hasattr(message, 'content') and message.content:
                        response_text = message.content

                # Print the final response
                if response_text:
                    print(f"Agent: {response_text}\n")
                else:
                    print("Agent: I encountered an issue processing your request.\n")

            except Exception as e:
                print(f"Agent: Sorry, I encountered an error: {str(e)}\n")

if __name__ == "__main__":
    asyncio.run(main())

Conclusion

You now have an Autogen assistant wired into Pinecone through Composio's Tool Router and MCP. From here you can:
  • Add more toolkits to the toolkits list, for example notion or hubspot
  • Refine the agent description to point it at specific workflows
  • Wrap this script behind a UI, Slack bot, or internal tool
Once the pattern is clear for Pinecone, you can reuse the same structure for other MCP-enabled apps with minimal code changes.
TOOLS

Supported Tools

Every Pinecone action and event your agent gets out of the box.

Cancel Bulk Import

Tool to cancel a bulk import operation in Pinecone.

Configure Index

Tool to configure an existing Pinecone index, including pod type, replicas, deletion protection, and tags.

Create Backup

Tool to create a backup of a Pinecone index for disaster recovery and version control.

Create Index

Tool to create a Pinecone index with specified configuration.

Create Index with Embedding Model

Tool to create a Pinecone index with integrated embedding model for automatic vectorization.

Create Index from Backup

Tool to create an index from a backup.

Create Namespace

Tool to create a namespace within a serverless Pinecone index.

Delete Index

Tool to permanently delete a Pinecone index.

Delete Namespace

Tool to permanently delete a namespace from a serverless index.

Describe Backup

Tool to retrieve detailed information about a specific backup.

Describe Bulk Import

Tool to describe a specific bulk import operation in Pinecone.

Describe Index Stats

Tool to get index statistics including vector count per namespace, dimensions, and fullness.

Describe Restore Job

Tool to get detailed information about a specific restore job in Pinecone.

Generate Embeddings

Tool to generate vector embeddings for input text using Pinecone's hosted embedding models.

Get Model Information

Tool to retrieve detailed information about a specific model hosted by Pinecone.

List Bulk Imports

Tool to list all recent and ongoing bulk import operations in Pinecone.

List Collections

Tool to list all collections in a Pinecone project (pod-based indexes only).

List Index Backups

Tool to list all backups for a specific Pinecone index.

List Indexes

Tool to list all indexes in a Pinecone project.

List Available Models

Tool to list all available embedding and reranking models hosted by Pinecone.

List Namespaces

Tool to list all namespaces in a serverless Pinecone index.

List Project Backups

Tool to list all backups for indexes in a Pinecone project.

List Restore Jobs

Tool to list all restore jobs for a project with pagination support.

List Vectors

Tool to list vector IDs in a Pinecone serverless index.

Query Vectors

Tool to perform semantic search within a Pinecone index using a query vector.

Rerank Documents

Tool to rerank documents by semantic relevance to a query.

Search Records in Namespace

Tool to search records within a Pinecone namespace using text, vector, or ID query.

Start Bulk Import

Tool to start an asynchronous bulk import of vectors from object storage (S3, GCS, or Azure Blob Storage) into a Pinecone index.

Update Vector

Tool to update a vector in Pinecone by ID.

Upsert Records to Namespace

Tool to upsert text records into a Pinecone namespace.

FAQ

Frequently asked questions

With a standalone Pinecone MCP server, the agents and LLMs can only access a fixed set of Pinecone tools tied to that server. However, with the Composio Tool Router, agents can dynamically load tools from Pinecone and many other apps based on the task at hand, all through a single MCP endpoint.

Yes, you can. Autogen fully supports MCP integration. You get structured tool calling, message history handling, and model orchestration while Tool Router takes care of discovering and serving the right Pinecone tools.

Yes, absolutely. You can configure which Pinecone scopes and actions are allowed when connecting your account to Composio. You can also bring your own OAuth credentials or API configuration so you keep full control over what the agent can do.

All sensitive data such as tokens, keys, and configuration is fully encrypted at rest and in transit. Composio is SOC 2 Type 2 compliant and follows strict security practices so your Pinecone data and credentials are handled as safely as possible.

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