Skip to main content

EndNote Online

Important things to know about syncing your EndNote Online and Desktop libraries

If you are an EndNote Desktop user you can sync your EndNote Desktop and EndNote Online libraries. All references, attachments and groups (but not Group Sets) will be displayed in EndNote Online. 

Important things to know about the sync process:

  • Before you sync for the first time ensure that you backup your EndNote library.
  • Even if you sync your EndNote Desktop Library with EndNote Online you should still regularly backup your EndNote Desktop Library. 
  • Sync only works with one EndNote Desktop library and EndNote Online account at the same time. 
  • Syncing EndNote Desktop with EndNote Online will inlcude all groups and group associations, but group sets, smart groups, and combination groups will not be displayed in your EndNote Online library. If you would like all Groups from the same Group set to be displayed together in your EndNote Online Library, you will need to give each Group in the Group set the same prefix. 

             For example, references from your Desktop Library shown on the left, will display in your EndNote Online Library as shown on the right:

              Group set in EndNote desktop       Groups in EndNote Online with group set prefix

  •  The sync process includes ALL changes to references in either library. For example, if you delete a reference in either the Desktop or Online library and then sync, the reference will be deleted from BOTH libraries. 
  • The first time you sync your library on another computer you should open a new, empty EndNote Desktop library and then sync. This will transfer all your references from your EndNote Online library into your EndNote Desktop library.

To sync you will need to:

  1. Set your preferences
  2. Sync your EndNote Online and Desktop libraries. 

Set your preferences

To allow EndNote Desktop and Online to sync:EndNote preferences box with Sync option selected

  1. In EndNote Desktop, go to Edit and Preferences
  2. Select Sync
  3. Click the Enable Sync button
  4. Enter the email address and password for your EndNote Online account
  5. Click on the OK or Save button
  6. You may be prompted to enter your name, address and other details to complete the integration of your Online and Desktop accounts
  7. You can tick the Sync Automatically checkbox to have Endnote automatically run the Sync process in the background every 15mins


Sync your EndNote Online and Desktop libraries

The sync process is always initiated from EndNote Desktop. Once you have set your preferences you simply need to click the Sync Library button in EndNote Desktop.

EndNote desktop toolbar with Sync button highlighted

Troubleshooting sync

If you experience issues with Sync, ensure that you:

  • Empty your Trash before syncing
  • Only sync with one EndNote Desktop library

If you are syncing on a different computer for the first time, open a new, empty EndNote Desktop library and then sync to download all your references from EndNote Online.

Sync Conflicts:

  • If there are any conflicts, a Sync Conflicts group will appear 
  • Right click on the group and select the Resolve Conflicts option. You can either choose to keep the EndNote desktop reference or the EndNote Online reference (the version of the reference you do not choose to keep is permanently deleted).  

Sync status:

Double click on Sync Status... in the group area to view information on the last Sync operation, including any errors such as storage limit, authentication or internet connection errors. 

How to reset Sync:

Follow these instructions on how to reset Sync if you want to clear your EndNote Online library and re-sync it with your Desktop library. If the references are correct in your EndNote Online account DO NOT follow these steps. Instead, simply make a new, blank EndNote desktop library and sync to that.