M365 Copilot Agent Suddenly Stopped Retrieving Documents from SharePoint Knowledge Source

Garapati Vinay 0 Reputation points
2026-09-22T13:07:03.71+00:00

Hi Team,

I have built an M365 Copilot Agent with a premium license. The agent uses a SharePoint document library as its knowledge source, which contains approximately 192,000 documents/items.

The agent was created in January 2026 and had been working as expected for several months. It was successfully retrieving relevant documents based on the agent instructions and performing its tasks correctly.

The agent was working correctly on September 7, 2026. However, starting on September 8, 2026, it suddenly stopped retrieving documents from the SharePoint knowledge source and is no longer able to complete its intended tasks.

We have thoroughly checked the environment and are confident that:

  • No permissions were changed.
  • No SharePoint access settings were modified.
  • No changes were made to the knowledge source configuration.
  • No significant changes were made to the agent itself.

The solution was working correctly before and appears to have stopped working unexpectedly.

Has anyone experienced a similar issue, or are there any known changes on the M365 Copilot side that could affect document retrieval from SharePoint knowledge sources?

We have been unable to identify the root cause and would appreciate any guidance or recommendations for troubleshooting this issue.

Microsoft 365 and Office | SharePoint | Development

4 answers

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  1. AI answer

    2026-09-22T13:07:25.4+00:00

    This pattern matches documented SharePoint knowledge-source failures where the agent returns no results without throwing an error, even when the configuration appears unchanged.

    The most relevant checks are:

    1. Verify user access to the exact SharePoint content
      • Copilot Studio respects Microsoft 365 security trimming.
      • Affected users must still have read access to the relevant sites and files.
      • Test by opening the exact SharePoint document path as the affected user.
      • Then run the same query with the same user account in Microsoft 365 Copilot Chat. If Copilot Chat also fails to retrieve the content, that points to a permission or search-indexing barrier rather than an agent-specific issue.
    2. Check the app registration and agent authentication scopes
      • If SharePoint knowledge is configured with manual authentication, the Microsoft Entra ID app registration must include at least Sites.Read.All and Files.Read.All.
      • Those scopes must also be present in the agent authentication settings together with profile and openid.
      • Required consent must be granted.
      • If scopes are missing from either the app registration or the agent settings, the agent can return no results and no errors.
    3. Confirm Restricted SharePoint Search is not blocking retrieval
      • If Restricted SharePoint Search is enabled for the tenant, SharePoint as a knowledge source is blocked regardless of app registration or agent configuration.
      • In that state, no results are returned until the relevant sites are added to the allowed list or the restriction is removed.
    4. Check whether the content is indexed
      • If the SharePoint content is not indexed by Microsoft Search, retrieval can be incomplete or fail.
      • Recently changed or large content sets can require time to appear.
      • Inconsistent results can also occur while semantic index synchronization is still catching up.
    5. Validate the SharePoint path and scope
      • Confirm the configured SharePoint site URL and library path are still correct and accessible.
      • If responses are slow or incomplete, narrow the search scope to specific sites or libraries and test with more specific queries.
    6. If this uses the SharePoint tool in Foundry or agent API scenarios, confirm identity mode
      • The SharePoint tool requires user identity passthrough.
      • Application-only authentication is not supported and can cause authentication failures.
      • Also confirm the user identity is in the same tenant as Microsoft 365.

    About known service-side changes:

    • No publicly documented change in the provided material indicates a platform update that should broadly disable previously working SharePoint knowledge retrieval.
    • A similar reported case was resolved after Microsoft addressed an internal service issue, so a service-side problem is possible when previously working agents and newly created agents both stop retrieving SharePoint knowledge without any tenant-side changes.

    A practical troubleshooting sequence is:

    1. Test one affected query in Microsoft 365 Copilot Chat using the same user.
    2. Open the exact SharePoint file directly as that user.
    3. Review the app registration permissions and the agent authentication scopes for Sites.Read.All, Files.Read.All, profile, and openid, and confirm consent is granted.
    4. Ask the SharePoint admin to verify Restricted SharePoint Search is not enabled for the tenant or blocking the relevant sites.
    5. Confirm the site/library path is still valid and the content is indexed.
    6. If both existing and newly created agents fail with the same SharePoint source and the checks above pass, treat it as a likely service-side issue.

    References:

    AI-generated content may be incorrect. Read our transparency notes for more information.

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  2. Jayden-P 3,130 Reputation points Independent Advisor
    2026-09-22T13:25:06.6333333+00:00

    Hi @Garapati Vinay

    To help narrow down the cause, could you please provide the following information?

    1. Is the issue affecting only this specific Copilot Agent, or do other agents that use the same SharePoint knowledge source exhibit the same behavior?
    2. When the agent responds, does it return no results at all, or does it return responses that appear to ignore the SharePoint content?
    3. Have you tested with a newly created agent connected to the same document library to determine whether the behavior can be reproduced?

    As an initial troubleshooting step, please try:

    • Removing and re-adding the SharePoint knowledge source if feasible.
    • Testing with a smaller SharePoint library to determine whether retrieval works in a different knowledge source.
    • Creating a new test agent that references the same library.
    • Verifying that the affected documents are still searchable through Microsoft Search and accessible to the account interacting with the agent.

    At this time, I am not aware of any documented change or known limitation that would specifically cause an existing Copilot Agent to suddenly stop retrieving content from an unchanged SharePoint knowledge source. However, I found a discussion from August where several users reported similar behavior, with Copilot Agents no longer returning content from their configured SharePoint knowledge sources despite no apparent configuration changes. While some users later indicated that the issue had been resolved, others reported that they continued to experience the same problem. The discussions can be found here:

    Please also give the AI answer a check as it can provide some helpful information especially this link: SharePoint knowledge sources don't return results in Copilot Studio

    Additionally, I would recommend opening a Microsoft support via Admin Center ticket so the engineering team can review backend indexing, retrieval logs, and any potential service-side issue.

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  3. Garapati Vinay 0 Reputation points
    2026-09-22T13:46:35.9233333+00:00

    Hi Jayden-P,

    Thank you for your response.

    Here is some additional information from our testing:

    The issue is not limited to a single agent. We have observed that all agents using SharePoint knowledge sources are unable to properly retrieve and process documents.

    The agents can sometimes identify a document when the exact file name is provided. However, instead of retrieving and processing the document content, the response only returns file metadata such as Created Date, Modified Date, Author, and other SharePoint properties.

    For example, when prompted with a specific file name (such as an Excel workbook), the agent responds with guidance like:

    "To extract every sheet, row, column, formula, and relevant shipment detail, attach the workbook directly in this chat or ensure the knowledge source indexes the workbook content rather than only its SharePoint/list metadata."

    This suggests the agent can locate the file reference but is not able to access or process the actual document contents.

    We have also created new test agents and configured them with smaller SharePoint knowledge sources, but the same behavior persists.

    Since the solution was functioning correctly until September 7, 2026, and no permissions, SharePoint settings, or knowledge source configurations were changed, this appears to be related to how the knowledge source content is being indexed or retrieved rather than an agent configuration issue.

    Has there been any recent change to SharePoint knowledge source indexing, document retrieval, or content processing behavior that could explain why only metadata is being returned instead of the document contents?

    Thanks for your help.

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  4. Evan Lang 0 Reputation points
    2026-10-02T18:29:45.69+00:00

    Hi,

    I had the same issue. My agent worked initially, but after about a day it started returning a 403 error when accessing files in its SharePoint knowledge source, even though no permissions had changed.

    I noticed the SharePoint site had a warning saying the site's content wouldn't be available to AI agents. I moved the same files to another SharePoint site that didn't have this warning and changed the agent's knowledge source to that site. It immediately started working again.

    Both sites are labeled private, so it doesn't appear to be simply a public vs. private Team issue. It may be related to SharePoint's Restricted Content Discovery setting. I'm still not sure why the restriction appeared after the agent had initially worked.

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