EndNote and Zotero are both powerful citation and reference management tools that work well with academic databases and add efficiency to scholarly writing. With institutional support for EndNote now at an end, the decision to stay with EndNote or to migrate to Zotero depends on your research style and what features matter most to you.

Before making a decision, consider if you:

• Collaborate in real time? Zotero supports synchronous collaboration, but only with other Zotero users.

• Want built-in PubMed search? EndNote lets you search directly within PubMed.

• Need live support? EndNote offers dedicated support while Zotero relies on community forums.

• Have time to learn? Zotero is user-friendly, but learning any new system takes time.

• Need syncing across devices? Zotero automatically syncs your library across your devices and to the cloud-based browser version. (Note: citation syncing across devices is free; file syncing requires paying for Zotero storage if over 300MB per account.)

• Save sources from the web? Zotero’s extensions capture citation data and PDFs from websites and databases.

• Need strong Word integration? EndNote uses fixed, unique citation IDs to maintain consistent links between references and citations. Zotero uses field codes to link citation data, but copying text between documents may break the link. 

Concerned about cost and storage?

If you have a digital library with many full-text documents, EndNote may be more cost-effective in the long term, especially if you already have a large EndNote library. EndNote’s one-time license purchase for the current version of the software includes three years of unlimited cloud storage. Zotero is free to download and use, but Zotero only includes 300 MB of free storage for citation file attachments; storage costs start at $20 per year and unlimited storage costs $120 per year. 

Decided to switch?

If you’ve decided to switch to Zotero, migrate your references and full-text attachments using XML format. However, custom fields and folder structures may not transfer cleanly; expect some manual reorganization.

Transition tips:

• Start small: Move a subset of references first.

• Clean as you go: Use this opportunity to organize your library.

• Take your time: Get comfortable with the new interface.