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EndNote for Windows - library will not close

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Summary:

A recurring issue has been reported in EndNote 2025.1 for Windows, where libraries cannot be closed using normal exit methods. The issue appears sporadic and can affect both local and cloud-stored libraries. The root cause has not yet been confirmed, but the issue is not believed to be user error and is under investigation by Clarivate.

Key actions and workarounds

Follow the steps below in order. The first two actions resolve most cases.

  1. Update or reinstall EndNote (recommended first step)
    • Uninstall EndNote.
    • Reinstall using the updated EndNote 2025.2 installer. This ensures all patch fixes are fully applied.
  2. Reset EndNote preferences (most effective)
  3. Check MS Word EndNote toolbar preferences. These settings can cause EndNote to reopen if Word continues running in the background. 
    In Word, open the EndNote tab and go to Preferences and disable:
    • Open EndNote when starting Word
    • Close EndNote when leaving Word 
  4. Verify library storage location.
    See this article for details: Storage location for EndNote libraries
    • Avoid syncing libraries directly from unsafe locations.
    • If needed, move the library to a new local folder and re-synchronise.
  5. Additional mitigations (case-by-case)
    • Temporarily disable antivirus or sync tools for testing purposes.
    • Repair the EndNote installation via Windows Programs & Features.
    • Create a new EndNote library and re-synchronise references.
    • Create a new Windows user profile if the issue persists system-wide.

Immediate workaround

  • Use Task Manager (Ctrl + Shift + Esc) to end the EndNote process when the library will not close.

Important notes

  • Restarting Windows usually resolves the issue temporarily only.
  • The issue has been observed with both local and OneDrive-stored libraries.

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