Zotero vs Mendeley vs EndNote
All three collect references, store your PDFs, and drop formatted citations into Word. The differences that actually decide it are cost, who owns your library, and which word processor you write in.
What a reference manager is for
A reference manager does three jobs: it captures a source from your browser in one click, it keeps the PDF and your notes attached to that record, and it inserts citations into your manuscript so the bibliography rebuilds itself when you add, delete, or reorder a source. The payoff is not the first citation — it's the day your supervisor says "the journal wants Vancouver, not APA" and you change it in a dropdown instead of over a weekend.
Here is how the three main options differ.
Zotero — free, open source, no vendor
Zotero is free and open-source software from the non-profit Corporation for Digital Scholarship. Version 7, released in August 2024, brought a redesigned interface and a reader that handles EPUBs and annotated web snapshots alongside PDFs.
- Storage: references, notes, tags and annotations sync free with no limit — only attached files count against your quota. Free accounts get 300 MB; paid plans are $20/year for 2 GB, $60/year for 6 GB, and $120/year for unlimited.
- Writing: plugins for Microsoft Word, LibreOffice and Google Docs ship with Zotero and install themselves on first launch. Google Docs support runs through the browser connector.
- Styles: Zotero uses Citation Style Language (CSL), whose crowdsourced repository offers over 10,000 free styles.
- Collaboration: group libraries are free, and Zotero does not charge extra for storage used by groups.
The catch is that Zotero leans on a plugin ecosystem for anything unusual — LaTeX users, for instance, typically add Better BibTeX rather than getting it out of the box.
Mendeley — Elsevier's option, strongest in Word
Mendeley is owned by Elsevier. The current app is Mendeley Reference Manager; the old Mendeley Desktop stopped being available for new downloads on 1 September 2022, and Elsevier has said it now receives essential maintenance only, with no new feature development.
- Storage: 2 GB free — the most generous free file allowance of the three — with paid upgrades available.
- Writing: Mendeley Cite is an add-in for Microsoft Word that works without the reference manager open, or even installed. There is no equivalent LibreOffice or Google Docs plugin.
- Capture: Mendeley Web Importer is a browser extension for Chrome and Firefox that pulls in references with their full-text PDFs.
If you write in Word on a managed university laptop and want the largest free PDF allowance, Mendeley is a reasonable default. If you have reservations about a major publisher hosting your reading history, that is a real consideration and Zotero is the answer to it.
EndNote — paid, institutional, style-heavy
EndNote is commercial software from Clarivate. The 2025 edition lists at roughly $275 for the full version and about $150 for the student edition (list prices as of August 2026), though many universities hold a site licence that makes it free to you.
- Styles: over 7,000 predefined output styles — the widest built-in coverage, which matters in fields with obscure journal formats.
- Writing: Cite While You Write in Microsoft Word, the workflow most established labs already use.
- New in 2025: Clarivate added AI features, including a Research Assistant that summarises and translates attached PDFs, plus journal matching.
- Storage: the desktop app pairs with an online account, but the terms differ between individual, student and institutional licences — check what yours actually includes.
So which one?
- Pick Zotero if you want free software with no vendor attached, or you write in LibreOffice or Google Docs. This is the right default for most students.
- Pick Mendeley if you live in Word, want 2 GB of free PDF storage, and don't mind Elsevier.
- Pick EndNote if your institution licenses it and your co-authors already use it. Matching your lab beats any feature comparison.
And the choice is reversible: all three import and export RIS and BibTeX, so a library moves cleanly. A half-written manuscript does not — citation fields belong to the plugin that inserted them — so switch between projects, not mid-draft.
Setting up a library is overkill for a single reference. Use our free citation generator to format one source in APA, MLA, Chicago, Harvard or IEEE and copy it straight into your draft.
What none of them do
A reference manager formats what is in the record. It does not check that the record is right — an import with a wrong year or a mangled author name produces a perfectly formatted wrong citation, so proof the fields when you save a source, not the night before submission.
More importantly, it cannot tell you whether a source exists. If you hand-key a reference an AI chatbot produced, your manager will format it beautifully and your marker will still find nothing when they search for it. Chatbots invent plausible references routinely, and a tidy bibliography does nothing to catch it.
Start from sources that are already real
CiteGood writes from real, retrievable papers and formats every citation as it goes — so there is nothing to verify after the fact.
Try CiteGood free →Frequently asked questions
Is Zotero really free?
Yes. Zotero is free and open-source software developed by the non-profit Corporation for Digital Scholarship. Syncing your references, notes, tags and annotations is free and unlimited; only attached files count against storage, and a free account gets 300 MB. Larger plans start at $20/year for 2 GB.
Is Mendeley Desktop discontinued?
Mendeley Desktop stopped being available for new downloads on 1 September 2022 and was replaced by Mendeley Reference Manager. Elsevier has said existing installations keep working and will receive essential maintenance, including critical security fixes, but no new features. New users should start with Mendeley Reference Manager.
Do I need to pay for EndNote?
EndNote is commercial software from Clarivate — the 2025 edition lists at roughly $275 for the full version and about $150 for the student edition. Many universities hold a site licence, so check with your library before buying: if your department already standardises on EndNote, that is usually the deciding factor.
Can I switch reference managers later?
Yes. All three import and export standard formats such as RIS and BibTeX, so moving a library is straightforward. Moving a half-finished manuscript is not — live citation fields are specific to each plugin — so switch between projects rather than mid-draft.
Will a reference manager guarantee my citations are correct?
No. It formats whatever is in the record, so imported metadata with a wrong year or a mangled author name produces a wrong citation. It also cannot tell you whether a reference exists at all, which matters if you typed it in from an AI chatbot's answer.