Skip to Main Content

EndNote@HKU: Sync EndNote Library with EndNote Online

Can I sync the library in my EndNote Desktop with an EndNote Online account?

Yes, you may sync your library in EndNote Desktop with an EndNote Online account. By doing this, you may access the library using different devices.

However, you may wish to note that an EndNote Online free account provides less function than EndNote Desktop. If you wish to enjoy all functions of EndNote Desktop, you are suggested to save your library as a compressed library for use on different devices. Click here for more details.

Kindly find the steps and some tips on syncing your library in EndNote Desktop with an EndNote Online account.

Before you sync

What would be sync?

You can only sync one EndNote Library on EndNote Desktop to one EndNote Online account. The data in your EndNote desktop and EndNote online account would be merged when you sync.

After the sync completes, you will have identical groups and references in both EndNote Desktop and EndNote Online (including the attachments and figures).

Syncing with EndNote Online includes all groups and group associations but group sets, smart groups, and combination groups will not be displayed in your online library.

ALL changes to the references in either library would be synced. 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.

Empty the trash

You are suggested to empty the trash in your library before you sync.

Backup your EndNote Library

You are suggested to backup your EndNote Library before you sync for the first time and also regularly after you sync your library with an EndNote Online account. Click here for steps to backup your EndNote Library.


1. Setting up your EndNote Online account

  1. Go to EndNote Online
  2. Click Register to setup a new account

2. Setting your preferences in EndNote Desktop

  1. In EndNote Desktop, go to Preferences
             (Windows)     Edit > Preferences
             (Mac)             Endnote 20 > Preferences
  2. Select Sync Enable Sync
  3. Enter the email address and password of your EndNote Online account
  4. Click the OK or Save button
  • You may be prompted to enter your name, address and other details to complete the integration of your online and desktop accounts.
  • Note: you can tick the Sync Automatically checkbox to have EndNote automatically run the sync process every 15 minutes in the background.

Mac sync

3. Sync your library in EndNote desktop with EndNote Online account

The sync process is always initiated from EndNote desktop.

In EndNote Desktop, go to Library > Sync

Tips and Troubleshooting

Sync your library in EndNote Online account with EndNote Desktop on another device

You should open a new, empty, EndNote library on the new device and then sync. All your references from EndNote Online will be downloaded into your new library. When you sync with that device again next time, you do not need to open a new blank library.

Sync Conflicts

Sync Conflict may occur if you edit a reference in both EndNote desktop and in EndNote online between Syncs. EndNote does not know which change you want to keep.

If it happens, a Sync Conflicts group will appear:

Right-click the group and select Resolve Conflicts. You can either keep the EndNote desktop reference or the EndNote Online reference (the version of the reference you do not choose to keep is permanently deleted).

You may also edit either reference and keep that edited version.

Sync Status:

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


Reset Sync

You may wish to reset because:

  • you wish to sync a different EndNote Desktop library with the EndNote Online account

  • you encounter complicated issues that you cannot fix

Before following the steps below, please ensure you backup your EndNote Desktop library first. Find steps to backup your library here.

To reset the sync:

  1. In the EndNote Desktop library, go to Sync.
             (Windows)     Edit > Preferences
             (Mac)             Endnote 20 > Preferences

    Uncheck Sync Automatically and then restart EndNote.

  2. Delete all references from EndNote Online by selecting the All checkbox under All My References and then click Delete.

  3. Delete all groups from EndNote Online, with the exception of any Shared Groups or ResearcherID Groups that may be setup by clicking on Organize Manage My Groups > Delete.

  4. Ensure you empty the Trash of both EndNote Dekstop and EndNote Online.

  5. In your EndNote Desktop library, go to Sync again and add #!resetLocalSync to the end of your email address
             (Windows)     Edit > Preferences
             (Mac)             Endnote 20 > Preferences

         Note: This is case sensitive - #!resetLocalSync
         e.g. if the email address was, change this to!resetLocalSync

  6. Click Apply and then OK.

  7. Start Sync again: Library > Sync

  8. EndNote will then appear to authenticate and return the prompt: 
          A Sync library can be linked to only one account.
          Do not proceed unless you intend to break the link to the original account.

  9. Click OK

  10. Another message will follow:
          Your local sync state has been reset. 
          Please re-enter your E-Mail Address, restart EndNote, and sync again.

  11. Click OK

  12. Go back to Sync and remove #!resetLocalSync from your email if you wish to sync your existing library.
             (Windows)     Edit > Preferences
             (Mac)             EndNote 20 > Preferences

    *If you wish sync another library with your online account, open the library in EndNote Desktop.

  13. Initiate Sync in EndNote Desktop and you will once again receive the following message:
          ‚ÄčA Sync library can be linked to only one account.
          Do not proceed unless you intend to break the link to the original account.

  14. Click OK and you will be prompted to make a backup.

  15. Click Yes and follow the prompts to do so since this is a different library.

  16. Your EndNote Online account in now sync with your opened library in EndNote Desktop.