Despite EndNote being one of the premier citation management systems, it was developed in the pre-Internet era (version 1 was released in 1989!), and relied on an internal desktop application. As it grew and updated, it failed to truly adapt to the technology of the 21st century. By the mid-2000s new web-based products were being developed (including Zotero), and EndNote had to quickly find a way to compete. It wasn't until 2007 that EndNote (owned by Thompson Reuters at the time) created a web-based version linked to ISI Web of Knowledge (now known at Web of Science), another product owned by Thompson Reuters.

Because of this historical oversight, there are significant limitations when it comes to sharing and collaboration with EndNote.

Sharing

• EndNote Desktop does not allow for the ability to directly share with colleagues. All sharing must be conducted by syncing to a web-based version.
• While both EndNote Libraries and EndNote Groups can be shared, there are differences in requirements, methodology, and access.
• Any sharing of libraries or groups from an EndNote Desktop account must be conducted in conjunction with a synced EndNote Online/Web account.
• Only one (1) EndNote Desktop library can be synced to a web-based EndNote account.

Word Processing

• EndNote's Cite While You Write ("CWYW") plugin only works with the desktop version of Microsoft Word (perpetual or subscription), it is not compatible with cloud-based products like Word Online or Google Docs, or from cloud-based Microsoft 365 (in Sharepoint).
• If using the subscription-based Microsoft 365, documents must be opened in Word desktop application to make any edits to the document.
• The CWYW plugin can only connect to either EndNote Desktop OR EndNote Online, but not both at the same time.
• Documents formatted with EndNote cannot be safely stored in cloud-based storage.
• Co-editing documents that are formatted with EndNote and are living outside of shared cloud-based storage (e.g. Sharepoint, Dropbox, Google Docs, etc.) can lead to the document becoming corrupted.

Changes in the new EndNote Web

Beginning with EndNote 21, a new cloud-based version of EndNote was launched. This new version was meant not as a stand-alone web-based version of EndNote but rather as a cloud-based storage solution, syncing the entire library (including PDFs, notes, and annotations), making them available on all devices.

One of the most important changes with the new EndNote Web is its compatibility with both Google Docs and Word Online. However, this new cloud-based product does not have many of the additional functionalities that EndNote Online Premium has, thus it really needs to be used as an expansion of the Desktop version.

• Create ONE (1) single library within your EndNote Desktop
  • .enl + .data  (library + data folder, on either Windows or Macs)
  • .enpl (packaged library, only available on Macs)
  • Use Groups and Group Sets to organize references
• Sync your single EndNote library to EndNote Online
• Create shared groups either in EndNote Desktop or EndNote Online and sync.
  • Invite collaborators to the shared group from within EndNote Online.
• Use the desktop application of Microsoft Word to add and edit EndNote citations to the Word document.Store Word documents in cloud-based storage like SharePoint, OneDrive, and DropBox as “unformatted” citations.
  • This allows for multiple people to edit the document without corruption and without the need to constantly email versions back and forth.
• Do not use Track Changes in Word with EndNote, it must be turned off (not visible) in order to format documents properly without errors.

In 2007, EndNote released EndNote Web, a web-based version of EndNote that was integrated in ISI Web of Knowledge (today known as Web of Science). 

Today, there are four separate web-based versions of EndNote. View a detailed comparison of all four versions here.

EndNote Basic

• EndNote Basic is a free web-only based reference manager that allows for up to a maximum of 50,000 references and 2GB of attachments.
• While it requires no additional purchases, subscriptions, or licenses, it has limited functionality (only the top 21 most commonly used citation styles, and a limited number of filters and connection files)

EndNote Online (with WOS)

• EndNote Online (with WOS) is a web-only based reference manager accessible only to users with a subscription to Web of Science (WOS)
• It can be accessed directly from within the WOS interface.
• It allows for up to a maximum of 50,000 references and 2GB of attachments.
• Compared to EndNote Basic, it has additional functionality, including citation styles, file formats, and connection files.

EndNote Online Premium

• EndNote Online Premium is the cloud-based portion of the licensed EndNote Desktop, available to all users who have purchased an EndNote Desktop version.
• It's only activated after an initial sync with the desktop application. 
• It allows for up to a maximum of 1 million references and unlimited file attachment storage. 
• It has full functionality, including over 7,000 predefined citation styles, 600+ accepted file formats, and over 3,000 connection files.
• However, only one desktop library can be synced to EndNote Online Premium.

EndNote Web

• EndNote Web is a NEW cloud-based portion of EndNote exclusive for Endnote 21 and EndNote 2025 users, that is activated from the initial sync in the desktop app.
• The new EndNote Web interface more closely reflects EndNote Desktop and will sync the entire library across all devices. 
• This new cloud-based EndNote is not meant as a stand-alone product, but rather to be used in conjunction with EndNote Desktop.
• Thus, it has less functionality that EndNote Online Premium, with limited accepted file formats, connection files, and sharing ability. 
• It allows for up to a maximum of 1 million references and unlimited file attachment storage, and over 7,000 predefined citation styles.
• It also is compatible with cloud-based word processors (Word Online and Google Docs).
• However, only one desktop library can be synced to EndNote Web.