Known Limitation: Microsoft Graph “20,000 Items” Bug

When Your OneNote Stops Syncing — What Large SharePoint Libraries Have to Do With It

For many organizations, OneNote notebooks stored in SharePoint or OneDrive are essential for collaboration. But in some cases, even small and well-structured notebooks can suddenly become inaccessible via Microsoft Graph API or fail to sync correctly in connected tools.

This issue often surprises users — especially when everything appears to be set up properly. In this post, we explain the technical background and what options are currently available to resolve it.

TL;DR

If your OneNote notebooks stop syncing or become inaccessible via API — even though they look fine — the issue may be caused by the SharePoint Document Library being too large.

  • SharePoint libraries have internal item count limits (5,000–20,000+), which vary depending on file types and metadata.
  • When these thresholds are exceeded, API access to OneNote can fail, even if the notebook itself is small and simple.
  • The solution: Move the notebook to a smaller library or reduce the size of the current one.
  • We’re actively investigating best practices and are happy to help — just open a support ticket if you need assistance with our Confluence OneNote integration.

What’s Happening Behind the Scenes?

Even if a notebook only contains a few pages, it doesn’t live in isolation. It’s stored inside a SharePoint Document Library, and Microsoft enforces internal item count limits on these libraries.

However — and this is important — the limit is not a fixed number. It seems to depend on the file types and how metadata is used:

  • Some libraries experience issues above 5,000 items, others above 10,000 or even 20,000.
  • The affected item count includes all files and folders, not just OneNote content.
  • When the threshold is exceeded, API access can fail — even though the notebook remains accessible via browser.

While Microsoft provides diagnostic tools and some guidance, the precise thresholds and triggers are still not consistently documented. Based on our testing and client cases, this limitation applies even when the notebooks themselves are small and simple.

Example from the Field

In one of our test projects, we encountered the following situation:

  • A OneNote notebook with just two sections and two pages became inaccessible via API.
  • The containing SharePoint Document Library held over 117,000 items.
  • Diagnostic tools showed the structure was technically supported — yet API access consistently failed.

This confirms that library size (and possibly content type configuration) can block API access, regardless of notebook size or structure.

What Can You Do?

Until Microsoft provides more clarity or architectural changes, we recommend the following workarounds:

1. Move the Notebook to a Smaller Library

Place the notebook in a separate SharePoint document library with a low item count. This usually restores full access and sync functionality immediately.

2. Reduce Library Size

If feasible, clean up the affected document library by archiving or deleting old items. Tools like PowerShell and Microsoft’s diagnostic scripts can help assess and manage item counts.

3. Plan Storage for Notebooks Proactively

If you’re integrating OneNote with external systems, store the notebooks in a dedicated, low-volume library from the beginning — especially in automation-heavy or integration-driven environments.

Still Under Investigation

We’re continuing to explore:

  • Whether shared links or specific permission setups might bypass the limitation
  • What undocumented internal limits affect notebook access
  • How we can ensure stable long-term access in large SharePoint environments

We’re also in exchange with Microsoft to better understand the architectural behavior behind these item count effects.

Need Help? Open a Ticket with Us

If you’re using our OneNote integration for Confluence and encounter this issue, or if you’re unsure how to structure your SharePoint to avoid it:

👉 Feel free to open a support ticket with us directly.

We’re happy to:

  • Check if your site is affected by item count limitations
  • Help you relocate your notebooks
  • Advise on sustainable setup options for your use case

This limitation may be subtle — but it’s solvable with the right structure. We’re here to help you make it work.

Posted by Jan Hendrik Winter
CraftCoders — Atlassian Integration Experts
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