When you try to migrate a large OneNote notebook from one SharePoint site to another, the process often fails without a clear error message. The migration tool may stop responding, show a generic failure, or skip items. This happens because OneNote notebooks have internal links, sections, and page content that exceed the size limits or timeout thresholds of standard SharePoint migration tools. This article explains why large notebooks fail and provides a safe, step-by-step method to migrate them without losing data or breaking internal links.
Key Takeaways: Migrating a Large OneNote Notebook Safely
- SharePoint Migration Tool (SPMT) chunking: Splits a notebook into smaller batches to avoid timeout failures.
- OneNote desktop app > Export to .onepkg: Exports the entire notebook as a single package file for manual re-import.
- SharePoint admin center > Content migration: Allows you to upload a .onepkg file directly to a target site collection.
Why Large OneNote Notebooks Fail During Migration
OneNote notebooks are not simple files. Each notebook is a folder structure containing section files (.one) and a table of contents that references every page. When you migrate a notebook using SharePoint Migration Tool or a third-party tool, the tool must process the entire folder structure and all its internal links. If the notebook exceeds a certain size — typically 2 GB or more — the migration process times out because the tool cannot finish the operation within the default 60-minute session limit.
Another common cause is the presence of embedded files or images that are larger than 250 MB. SharePoint blocks uploads of individual items larger than that threshold. The migration tool may fail silently when it encounters such an item, leaving the notebook partially migrated or completely skipped.
Finally, the notebook’s internal link structure can break if the migration tool renames the notebook or changes its URL. This results in a notebook that opens but shows broken links to sections and pages.
Size Limits That Trigger Failures
The following limits are relevant to OneNote migration:
- Maximum notebook size: 2 GB for SPMT processing without chunking.
- Maximum single file upload to SharePoint: 250 MB.
- Maximum number of pages per section: 1000 (migration may skip pages beyond this).
- Default SPMT session timeout: 60 minutes.
Step-by-Step Fix: Migrate a Large OneNote Notebook Without Failure
Use one of the two methods below. Method 1 is faster for notebooks under 5 GB. Method 2 works for any notebook size but requires OneNote desktop app.
Method 1: Use SharePoint Migration Tool with Chunking
- Download and install SPMT
Go to the Microsoft 365 admin center and search for SharePoint Migration Tool. Download the latest version from the official Microsoft site. Install it on a Windows 10 or Windows 11 computer that has at least 8 GB of RAM. - Open SPMT and create a new migration task
Launch SPMT. Click Start and then select OneDrive or SharePoint as the source. Choose SharePoint as the destination. Enter the source site URL and the destination site URL. - Select the notebook folder
In the source selection screen, navigate to the OneNote notebook folder. The folder name ends with .one. Select it. Do not select individual .one files — select the whole folder. - Enable chunking in advanced settings
Click Advanced and scroll to Migration behavior. Set Chunk size (MB) to 500. This splits the notebook into 500 MB batches. Set Maximum concurrent uploads to 3 to avoid overwhelming the network. - Start the migration
Click Start and monitor the progress. SPMT will process each chunk separately. If a chunk fails, SPMT retries automatically up to three times. After completion, verify that all sections appear in the target site.
Method 2: Export Notebook to .onepkg and Import via SharePoint Admin Center
- Open the notebook in OneNote desktop app
Launch OneNote 2016 or OneNote for Windows 10. Open the notebook that failed during migration. Ensure all sections and pages are fully synced by checking the sync status icon in the upper-right corner. - Export the notebook as a .onepkg file
Click File > Export. Under Export current, select Notebook. Click Export. Choose a local folder and save the file. The .onepkg file packages the entire notebook structure into one file. - Upload the .onepkg to the target SharePoint site
Go to the target SharePoint site where you want the notebook. Navigate to the document library. Click Upload > Files and select the .onepkg file. SharePoint extracts the notebook automatically. This process may take several minutes for large files. - Verify the imported notebook
Open the notebook from the SharePoint library. Check that all sections and pages are present. Test internal links by clicking between sections. If any links are broken, use the OneNote desktop app to relink them manually by editing the hyperlink in the section tab.
If the Notebook Still Has Issues After Migration
Notebook Opens But Shows Missing Sections
This usually means the chunking process skipped some files. Open the source notebook in OneNote desktop app and compare the section list with the migrated notebook. Export the missing sections individually by right-clicking the section tab and selecting Export > Section. Upload the exported .one file to the same library. The notebook will merge the new section automatically.
Internal Links Point to the Old Site
When you migrate a notebook, links to pages within the notebook retain the old site URL. To fix this, open the notebook in OneNote desktop app. Press Ctrl+F to search for the old site URL. Right-click each linked page and select Edit Link. Replace the old URL with the new site URL. This step is manual but necessary for large notebooks with many cross-references.
Migration Tool Reports File Size Exceeded Limit
If SPMT reports that a file exceeds 250 MB, locate that file in the source notebook. Open the source notebook and remove large embedded files. Common culprits are scanned PDFs or video files pasted directly into a page. Save the large file separately in a document library and insert a link to it instead. Then re-run the migration with chunking enabled.
SPMT Chunking vs .onepkg Export: Key Differences
| Item | SPMT with Chunking | .onepkg Export and Import |
|---|---|---|
| Notebook size limit | Up to 5 GB with chunking | No limit (file upload limit is 15 GB in SharePoint but import may be slower above 10 GB) |
| Internal link preservation | Preserves links within the same site | Breaks links to old site URL; manual fix required |
| Required software | SPMT installed on Windows | OneNote desktop app and SharePoint browser |
| Time to complete | Faster for notebooks under 2 GB | Slower for notebooks over 5 GB due to upload time |
| Retry on failure | Automatic retry up to 3 times | Manual re-upload required if file upload fails |
Choose SPMT with chunking if you need to preserve internal links and have a notebook under 5 GB. Choose .onepkg export if the notebook is larger than 5 GB or if SPMT repeatedly fails.
After completing the migration, test the notebook by opening it in OneNote for the web and the desktop app. Verify that all sections load and that the table of contents updates correctly. If you used the .onepkg method, run the link-fixing procedure described above to restore cross-references. For ongoing management, consider splitting very large notebooks into smaller ones organized by year or topic to avoid future migration failures.