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MrRudy's avatar
MrRudy
Occasional Reader
Jan 14, 2026

Copilot Studio Agent vs SharePoint subfolders

Hi community,

 

We are exploring the Copilot Studio Agents and are running into some issues. When we add the root library of a SharePoint site the agent is able to search the documents within, however when using only a subfolder of the site as a knowledge source it can't find any documents. The agent response is:

"I have searched the available knowledge base but could not find any instructions on "Subject XXX". 

 

I read it can take up to 24 hours to build the index for subfolders, however after 3 days of waiting the agent still can't find any documents. I've tried making a new agent directly adding the subfolder as a source. The permissions of the user configuring the agent are also correct and the user has full access to all the files. I've also tried working with subagents with no success either.

 

Has someone else experienced the same and is it correct agents can't work properly yet with subfolders of SharePoint sites?

 

 

Copilot in SharePoint
microsoft 365 copilot
troubleshooting

1 Reply

  • BrianStephen's avatar
    BrianStephen
    Icon for Microsoft rankMicrosoft
    Jan 14, 2026

    Copilot Studio does not reliably index or retrieve content when a subfolder is added on its own. In contrast, full sites and full document libraries index and respond correctly.

    Although SharePoint agents support folders as knowledge sources, Copilot Studio and SharePoint agents still use different ingestion models. The SharePoint FAQ confirms that integration with Copilot Studio is still in progress and that the two systems do not yet share complete indexing behavior. 

    Why This Happens

    Copilot Studio depends on the SharePoint search index, which consistently provides full-site and full-library indexing but does not reliably produce complete index payloads for isolated subfolders. As a result, Copilot Studio cannot find documents even though they are accessible to the user and visible in the SharePoint UI.

    There is no published Microsoft documentation that indicates this limitation has been resolved as of 2026. The ingestion model remains unchanged.

    Recommended Workarounds

    To ensure content is discoverable:

    1. Add the entire document library as the knowledge source.
    2. Create a dedicated, smaller library if you need tighter scoping.
    3. Add individual files when necessary (up to supported limits).

    Conclusion

    This behavior is expected given the current product architecture. Subfolders alone are not reliably indexed by Copilot Studio agents, and Microsoft has not yet documented support for this configuration. The recommended approach is to use libraries, sites, or individually selected files until deeper SharePoint–Copilot Studio integration is completed.

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