Zotero vs Mendeley vs EndNote: Choosing a Reference Manager

All three store references and format bibliographies. The real differences are cost, which word processors they support, who owns them, and how hard it is to leave.

Explainer · 8 min read · Directive Publications Editorial Team

The short answer

All three tools do the same core job. They collect references from databases and web pages, store PDFs, insert citations into your manuscript, and format the bibliography in whatever style the journal requires. For most early-career researchers, any of them will work.

The differences that matter are practical:

• Zotero is free, open source and run by a nonprofit. It works with Word, LibreOffice and Google Docs.
• Mendeley is free to use with a 2 GB storage allowance and is owned by Elsevier. Its current citation tool works in Microsoft Word only.
• EndNote is paid software from Clarivate, often provided through a university licence. It works with Word, Google Docs and Apple Pages.

If you have no constraints at all, Zotero is the lowest-risk default because it costs nothing and is easy to leave. But most people do have constraints, and the rest of this post shows how to weigh them.

How the three compare

Storage allowances, prices and features change, so confirm the current terms on each vendor's site before you commit.

Zotero: free, open, and portable

Zotero describes itself as a free, open-source research tool. It was created at the Roy Rosenzweig Center for History and New Media at George Mason University and is now developed by the Corporation for Digital Scholarship, a nonprofit.

What that means for you:

• Cost. Syncing your library data (items, notes, tags, collections) is free and unlimited. Syncing attachment files such as PDFs uses Zotero Storage, which includes 300 MB free. You can buy more, or sync personal library files through your own WebDAV server instead.
• Writing. Plugins for Word and LibreOffice are bundled with the app, and Google Docs support comes through the Zotero Connector browser extension. That matters if any co-author drafts outside Word.
• Styles. Zotero uses the Citation Style Language, whose open repository holds over 10,000 free styles. Medical journals that follow Vancouver or a house variant are usually covered, and you can edit a style if needed.
• Retractions. Zotero checks items with a DOI or PMID against Retraction Watch data, flags retracted items in your library, and warns you if you try to cite one through the word processor plugin.
• Groups. Group libraries have no member limit. If group file storage is enabled, files count against the group owner's quota, and group libraries cannot use WebDAV.

The trade-off is that you manage it yourself. There is no institutional support desk, although many university libraries teach it.

Mendeley: free storage, Word-only citing

Elsevier acquired Mendeley in 2013. The current desktop and web product is Mendeley Reference Manager. The older Mendeley Desktop receives no further updates, so do not start a new library there.

According to Elsevier's Mendeley support pages, a free account includes 2 GB of personal storage, 100 MB of shared storage across all groups, and up to 5 groups of up to 25 collaborators. Upgrades add personal storage only, not shared space.

For writing, Mendeley's citation add-in is Mendeley Cite. Elsevier states that it is currently available only for Microsoft Word, including Word online. It works as a standalone add-in, so co-authors can use it without installing the full reference manager. LibreOffice users have only the plugin from the discontinued Mendeley Desktop. Mendeley Cite offers no Google Docs option.

Mendeley is a reasonable choice if you write in Word, want generous free storage, and your group already uses it. Think twice if any co-author drafts in Google Docs or LibreOffice.

EndNote: institutional, Word-centred, paid

EndNote is Clarivate's commercial reference manager. Many universities license it, so check with your library before buying a copy. Clarivate offers a free trial, and a more limited online version exists alongside the desktop software.

Its strengths:

• Cite While You Write. The citation tool works in Microsoft Word, in Google Docs through an add-on (this needs a library synced to an EndNote Web account and EndNote 21 or later), and in Apple Pages on a Mac.
• Styles. EndNote says it gives access to over 7,000 citation styles.
• Retraction alerts. When you are signed in and syncing, EndNote checks references with a DOI or PMID against the Retraction Watch database, collects retracted items in a dedicated group, and flags them when you insert citations in Word.

One habit to learn early: a desktop EndNote library is a .enl file plus a matching .Data folder, and the two must stay together. EndNote's own documentation warns that uncompressed libraries should not be used in cloud-syncing folders such as OneDrive, iCloud or Dropbox, because of the risk of corruption. To move a library, use a compressed library file or EndNote's own sync.

Five questions that settle the choice

Work through these in order. The first one that gives a clear answer usually decides it.

1. What do your co-authors use? Shared manuscripts work best when everyone cites with the same tool. If your lab or supervisor has a standard, adopt it unless you have a strong reason not to.
2. Which word processor do you draft in? If anyone on the team uses Google Docs, Mendeley Cite will not work for them. If anyone uses LibreOffice, Zotero is the only one of the three with a current plugin for it.
3. Does your institution pay for EndNote? If it does, cost stops being a reason to avoid it. If it does not, ask yourself whether you will keep paying after you leave.
4. How many PDFs will you store? A large library of PDFs will outgrow Zotero's 300 MB of free storage sooner than Mendeley's 2 GB. Zotero's free, unlimited data sync still covers the references themselves, and a WebDAV server can carry the files.
5. How easily can you leave? Your library will follow you across several jobs. Favour a tool that exports cleanly and that you could replace without losing years of notes.

Whichever tool you choose, use one per manuscript. Mixing citation plugins in a single document is a reliable way to break the bibliography.

Switching later: what moves and what doesn't

You are not locked in, but moving is not free of effort.

• Mendeley to Zotero. Zotero imports directly from Mendeley's online library, keeping folders and attached files, provided everything has synced to Mendeley's servers first. The Zotero import guide explains that Zotero can relink citations created by the old Mendeley Desktop plugin, but citations created with Mendeley Cite are not readable by Zotero.
• EndNote to Zotero. Export from EndNote as EndNote XML and import that file. Zotero looks for attachments relative to where the XML file is saved, so save it in the right place or the PDFs will not come across. Fields Zotero does not support are added as notes.
• Any direction. All three can exchange references through standard formats such as RIS. Mendeley Reference Manager, for example, exports to BibTeX, RIS and EndNote XML. References move easily; live citations inside existing Word documents often do not.

The practical rule: switch between projects, not in the middle of one. Finish the manuscript you are working on in the tool that inserted its citations, then migrate.

Habits that matter more than the tool

A reference manager only formats what you feed it. A wrong author list or title in your library becomes a wrong reference in every paper that cites it.

• Check every imported record. Browser capture tools sometimes grab the wrong title, miss authors, or misread a preprint as the journal version. Fix the record once and every future citation is correct.
• Keep DOIs and PMIDs filled in. Both Zotero and EndNote rely on them for retraction checks, and some journals ask for DOIs in the reference list.
• Use the journal's own style, then check it. Select the journal's style if one exists, then compare a few references against the instructions for authors. Our manuscript submission checklist covers what else to check before you upload.
• Cite more than papers. Datasets, software and code need proper records too. See citing data, software, and code for how to build those entries.
• Back up your library. Export a full copy now and then, independent of any sync service.

If a retraction warning appears for a paper you have already cited in published work, our guide to correcting the published record explains your options.

Directive Publications links its author guidelines, which explain how to prepare, structure and format a manuscript, from its For Authors page. Read them before you start writing, so your reference manager is set to the right style from the first citation rather than at the proof stage.