Configure MCPs for Benchling AI

Stuart
Stuart
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Quick Reference:

  • MCP Help Pages
  • MCP URLs
    • Benchling MCP Server URL format: https://<tenant>.mcp.benchling.com/mcp
    • Benchling MCP Redirect (or callback) URI format: https://<tenant>.benchling.com/1/api/llm/mcp/oauth/callback 

Overview

MCPs allow Benchling AI to access data from external systems like Microsoft Teams, SharePoint, Slack, and other platforms that support the Model Context Protocol (MCP). This extends Deep Research's ability to provide comprehensive answers by incorporating information from multiple sources across your organization's data ecosystem. MCPs work by establishing secure connections between Benchling and external MCP servers, allowing Deep Research to retrieve relevant information while respecting your authentication and permissions in those systems.

Deep Research must be enabled on your tenant to use MCPs.

Note: MCPs currently work with Deep Research only. Deep Research automatically determines which connected systems to query based on your prompt.

 

Configure MCPs

Before MCPs are available for users to enable, tenant admins must first set up the MCP for the tenant. 

To configure an MCP:

  1. Click the Connections side panel
  2. Click the MCPs tab
  3. Click the + icon to create a new MCP
  4. Complete the MCP configuration:
    • Name: Enter a descriptive name for the MCP (this is the name that will be visible to users)
    • Server: Enter the MCP server URL (typically ends in /mcp for HTTP connections or /sse for SSE connections)
    • Type: Select the connection type
      • [Default] Use HTTP for most connections (URLs ending in /mcp)
      • Use SSE for server-sent events connections (URLs ending in /sse)
      • If you're unsure, start with HTTP and try SSE if the connection doesn't work
  5. Review the available tools from the MCP server and select which tools users can access
  6. Click Save

For example, to connect to Notion you might enter https://mcp.notion.com/mcp as the server URL and select HTTP as the type. To connect Deep Research in one tenant to another tenant, you can use the Benchling MCP url format like https://<tenant>.mcp.benchling.com/mcp

See Benchling MCP for more on setting up and using Benchling's MCP Server.

 

Common settings:

  • Benchling MCP Redirect (or callback) URI or URL: https://<tenant>.benchling.com/1/api/llm/mcp/oauth/callback 

 

Manage tenant MCPs

After creating a MCP, admins can adjust settings or remove access. Note, the settings for admins to adjust the behavior for their tenant and to adjust the behavior for themselves as a user are both managed through this page. These settings will be present for tenant admins only:

  • Admin settings: Adjust configuration settings for the connector for the entire tenant, including which tools are available to users
  • Delete: Remove the connector for all users on the tenant

Instructions for setting up MCPs as a user can be found in the Deep Research article. 

 

Frequently asked questions

  • What types of external systems can I connect?
    • You can connect to any system that provides an MCP server. Common examples include Microsoft Teams, SharePoint, Slack, and other collaboration or data platforms. The system must provide an MCP server URL for the connection.
  • Why am I getting an authentication error?
    • If you encounter authentication errors when setting up your connection, the external system may require pre-registration of the connection on the MCP server side. Contact Benchling Support for assistance with authentication issues.
  • Which Benchling features work with MCPs?
    • MCPs currently work with Deep Research only. You cannot use MCPs with Ask or other AI features at this time.
  • Do MCPs require additional licensing?
    • MCPs don't require additional licensing beyond your existing Benchling license. However, your tenant must have Deep Research enabled to use MCPs. Depending on the MCP, you may be required to have a license to the external system. 

 

Example Setup Process

 

Set up the Sharepoint MCP 

  • Important notes:
    • Microsoft offers many MCP options, many of which are still in a beta or preview state as of April 2026
    • Your sharepoint administrator may need to work with Microsoft to request that some MCP offerings or features be enabled before they can be set up
    • This is a walkthrough of the steps required to set up the Microsoft "Work IQ MCP" server for SharePoint
      • As of April 2026, it is recommended that you set up at least the Work IQ Sharepoint, Work IQ Copilot, and Work IQ Word (provides additional features specifically for Word documents) servers. 
        • You can optionally also enable any of the other MCP servers(e.g. User, Mail, Calendar, Teams, OneDrive) that may be valuable for your users
      • Note, Microsoft currently limits file operations to files ≤5MB
        • Larger files may be able to be identified via search tools provided by the Copilot server, but their full contents may not be able to be brought over through the Sharepoint MCP server. 
    • Work IQ MCP server URLs are formatted like:
      • https://agent365.svc.cloud.microsoft/agents/tenants/{tenant-id}/servers/{server-name}
      • {server-name} = mcp_SharePointTools for Sharepoint, mcp_M365Copilot for Copilot search; mcp_WordServer for Word
  • Requirements:
    • For a user to be able to use any of the MCP servers with Benchling AI, they will need: 
      • A Microsoft 365 Copilot license
        • Standard M365 E3 or E5 licenses alone are insufficient. 
        • After assignment, features may take up to 24 hours to propagate.
      • Entra ID admin consent
      • A service principal provisioned in the tenant
      • Office update channel must be set to Current Channel or Monthly Enterprise Channel 
        • Semi-Annual is not supported
  1. [Entra Admin] Provision service principals in the tenant
    1. [Entra Admin] You must create a service principal for each MCP service and grant consent for the permissions needed for each.
      1. Microsoft provides an open source CLI with helpful instructions for performing and/or automating this step. 
    2. [Entra Admin] Grant admin consent in Entra ID
      1. Navigate to the Microsoft Entra admin center → Enterprise applications → search for "Agent 365 Tools" → API Permissions → grant admin consent. 
      2. For each MCP server your organization wants to enable, the corresponding scope must be consented. 
        1. The critical scopes for the servers above are McpServers.OneDriveSharepoint.All (SharePoint), McpServers.Word.All (Word), and McpServers.Knowledge.All (Copilot Search).
      3. [Entra Admin] Configure governance in the M365 Admin Center. 
        1. Go to the Microsoft 365 Admin Center → Agents and Tools section. 
        2. Here you can view all activated Work IQ MCP servers, allow or block specific servers per organizational policy, and apply scoped permissions.
      4. [Entra Admin] Enable security prerequisites. 
        1. Ensure Unified Audit Logging and Multi-Factor Authentication are enabled tenant-wide. 
        2. Configure Conditional Access policies as appropriate. 
  2. Your Benchling Admin and Entra admin will work together for these final steps:
    1. Your Benchling admin should ask your Entra admin for your tenant ID if you do not already know it. 
    2. For each MCP server:
      1. [Benchling Admin] Navigate to Benchling > avatar (bottom left corner) > Tenant Admin Console > Customize > + Create custom MCP
      2. [Benchling Admin] Give it a clear name (this is what your end users will see in Benchling) like "Sharepoint" or "Copilot"
      3. [Benchling Admin] Populate the Server URL 
        1. e.g. for sharepoint: https://agent365.svc.cloud.microsoft/agents/tenants/{tenant-id}/servers/mcp_SharePointTools
      4. [Benchling Admin] Leave Transport Type as the default "Streamable HTTP"
      5. [Benchling Admin] Expand the Manual OAuth registration box
      6. [Benchling Admin] Copy the redirect URI and share it with your Entra admin
      7. [Entra Admin] Register Benchling as an OAuth client in Entra ID.
        1. Navigate to the Microsoft Entra admin center → App registrations → New registration. Give it a name like "Benchling AI Connector" and set the redirect URI from your Benchling admin. Typical format:
        2. https://{your-subdomain}.benchling.com/1/api/llm/mcp/oauth/callback
        3. [Entra Admin] Under Certificates & secrets, generate a new client secret and copy the value immediately (it won't be shown again). Note the Application (client) ID from the Overview page — you'll need both values for the Benchling configuration.
        4. [Entra Admin] Under API permissions, add the delegated permissions for the Work IQ servers you want to enable: McpServers.OneDriveSharepoint.All, McpServers.Word.All, and/or McpServers.Knowledge.All and any others you choose. 
        5. Grant admin consent for these permissions.
      8. [Benchling Admin] Expand the Manual OAuth registration section:
        1. Redirect URI: This is pre-populated by Benchling (e.g., https://{subdomain}.benchling.com/1/api/llm/mcp/oauth/callback). You should have already registered this URI in your Entra ID app registration in the previous step.
        2. Client ID: Paste the Application (client) ID from your Entra ID app registration
        3. Client Secret: Paste the client secret value you generated in Entra ID
      9. Expand the OAuth provider overrides section:
        1. Authorization URL: Replace {tenant} with your Microsoft 365 tenant ID: https://login.microsoftonline.com/{your-tenant-id}/oauth2/v2.0/authorize
        2. Token URL: Same substitution: https://login.microsoftonline.com/{your-tenant-id}/oauth2/v2.0/token
        3. Suppress resource parameter: Check this box 
      10. Click Add. Repeat for each additional Work IQ server (Word, Copilot Search) using the same Client ID and Client Secret but a different Server URL and Name.

 

 

 

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