Comparison

Free Reference Managers Compared: Zotero vs Mendeley

Zotero, Mendeley, EndNote, JabRef and Paperpile compared on price, free storage, Word and LaTeX support and openness, with official sources.

Sciicons · Published October 11, 2026 · Last updated October 11, 2026

Last updated: October 11, 2026. All prices and limits were checked against the official pages linked below on this date.

Quick answer: Zotero is the best free reference manager for most researchers: it is open source, has unlimited local storage, 300 MB free cloud sync and plugins for Word, LibreOffice and Google Docs. JabRef suits LaTeX users, Mendeley offers 2 GB free cloud storage, and EndNote makes sense when your institution pays.

What is the best free reference manager?

• Best overall free reference manager: Zotero. Free and open source, unlimited local storage, 300 MB of free cloud file sync, and plugins for Word, LibreOffice and Google Docs.
• Best for LaTeX/BibTeX users: JabRef. Free, MIT-licensed, works directly on .bib files.
• Best free cloud storage allowance: Mendeley. 2 GB personal storage on a free account.
• If your institution pays for it: EndNote Desktop. A powerful option many universities license; otherwise EndNote Basic is free but more limited.
• Paid but polished, browser-first: Paperpile. No free plan (30-day trial); academic pricing from about $4.15/month billed annually.

Where can you find papers before managing them?

Ocean of Papers

Ocean of Papers is a free academic search engine that searches OpenAlex, PubMed, arXiv, bioRxiv, medRxiv and Europe PMC together, lets you explore citations and download open-access PDFs, with no account needed. Use it to find papers, then save them to the reference manager you choose below.

How do free reference managers compare? Comparison table

Sources for each cell are given in the sections below; cells marked (unverified) could not be confirmed on an official page on the date of checking.

Is Zotero the best free reference manager?

Zotero is developed by the nonprofit Corporation for Digital Scholarship (storage page) and released as open source under AGPLv3 (source code).

Storage. Each user gets 300 MB of free online file storage. Paid plans are 2 GB for $20/year, 6 GB for $60/year and unlimited for $120/year (individual storage). The quota applies only to files synced to Zotero's servers; you can store unlimited files locally (storage FAQ). Group libraries draw from the group owner's storage at no extra charge (storage).

Writing. Official plugins support Word, LibreOffice and Google Docs (word processor plugins, Google Docs), with thousands of CSL citation styles.

Strengths: free, open, a strong browser connector for saving papers from journal pages, a built-in PDF reader with annotations, and a large plugin ecosystem.

Trade-offs: cloud file sync beyond 300 MB requires a paid plan or WebDAV.

Is Mendeley still free?

Elsevier's Mendeley Reference Manager is free for Windows, macOS and Linux, and on the web; the older Mendeley Desktop still runs but receives only essential maintenance (Mendeley, Oxford LibGuide).

Free account includes (Mendeley support):

• 2 GB personal storage
• Up to 5 groups of up to 25 collaborators
• 100 MB shared storage across groups

Writing: Mendeley Cite works with Microsoft Word, including Word Online (migration help).

Trade-offs: the library lives primarily in the cloud (files can be downloaded for offline use), and the desktop app does not run on 32-bit computers (same source).

Is EndNote free?

EndNote Basic (online) is free to anyone, with up to 50,000 references and 2 GB of attachments (Clarivate comparison, Wayne State guide). It lacks some desktop features such as one-click Find Full Text (University of Iowa guide).

EndNote 2025 Desktop is a one-time purchase listed at $275 (full), $150 (student, with proof of enrollment) and $125 (upgrade from EndNote 21 or earlier). One license covers one person on up to three machines, and a free trial is available (EndNote buy page).

Tip: many universities provide EndNote Desktop free to staff and graduate students (example: University of Iowa). Check your library before buying.

Is JabRef good for LaTeX users?

JabRef is free, open-source software under the MIT License for Windows, macOS and Linux. It works directly on BibTeX/BibLaTeX .bib files without a proprietary database (license, GitHub).

Best for: LaTeX and Overleaf workflows, where the .bib file is the source of truth and can be version-controlled with Git.

Trade-offs: no hosted cloud sync; put the .bib file in your own synced folder or repository.

Is Paperpile worth paying for?

Paperpile is a browser-based manager integrated with Google Drive and Google Docs. It has no free plan but offers a 30-day trial; the academic Regular plan is listed at about $4.15/month billed annually ($49.80/year) (pricing, subscriptions explained).

What should you look for in a reference manager?

Before comparing brands, decide which of these matter for your work:

• Capture: how easily it saves a paper's metadata and PDF from a journal page, PubMed or a DOI. Browser connectors (Zotero, Mendeley, Paperpile) do this in one click.
• Writing integration: a plugin for the editor you actually use (Word, Google Docs, LibreOffice or LaTeX). This is where the tools differ most.
• Citation styles: journals use different styles. Zotero and other CSL-based tools can switch styles in seconds; check that your target journal's style exists.
• Storage and sync: whether you need PDFs on several computers, and how large your library is likely to grow over a PhD or a career.
• Collaboration: shared group libraries for lab members or co-authors, and whether every collaborator needs an account.
• Lock-in and longevity: open formats and export options (RIS, BibTeX, CSL JSON) protect years of curated references if a product changes or is discontinued.
• Cost over time: a free tool with a small paid storage add-on can cost less over five years than a one-time license, or more, depending on your library size.

Which reference manager should you choose?

You write in Word or Google Docs and want free

Zotero. It is the only free option here with official plugins for Word, LibreOffice and Google Docs.

You write in LaTeX

JabRef, or Zotero with the Better BibTeX plugin (a third-party plugin; check compatibility with your Zotero version).

Your PDFs exceed 300 MB and you want free sync

Mendeley (2 GB free) or Zotero with your own WebDAV storage.

Your institution has a site license

EndNote Desktop is a reasonable choice when it is provided free, especially if colleagues already share EndNote libraries.

Your lab collaborates on a shared library

Zotero group libraries (storage from the owner's quota) or Mendeley groups (5 groups of 25 on free accounts).

How do you switch between reference managers?

• Mendeley → Zotero: Zotero has a built-in Mendeley importer; test on a small library first.
• EndNote → Zotero or JabRef: export as RIS or BibTeX; check PDF links and notes afterwards.
• Always back up before migrating (export your library to RIS or BibTeX).

Where do figures fit in?

Reference managers handle citations, not visuals. If you also need schematic figures for the same manuscript, keep credits for openly licensed images (for example from Sciicons, Servier Medical Art or NIH BioArt) alongside your references, because CC BY assets need attribution in the figure legend or acknowledgments.

Sources

• Zotero individual storage: https://www.zotero.org/support/individual_storage
• Zotero storage FAQ: https://www.zotero.org/support/storage_faq
• Zotero source code (AGPLv3): https://www.zotero.org/support/dev/source_code
• Zotero word processor plugins: https://www.zotero.org/support/word_processor_integration
• Zotero Google Docs: https://www.zotero.org/support/google_docs
• Mendeley free account: https://service.elsevier.com/app/answers/detail/a_id/18206/supporthub/mendeley/
• Mendeley future: https://www.mendeley.com/the-future-of-mendeley
• EndNote buy page: https://endnote.com/buy/
• EndNote Online comparison (Clarivate): https://support.clarivate.com/Endnote/s/article/EndNote-Online-Comparison
• JabRef license: https://docs.jabref.org/advanced/license
• Paperpile pricing: https://paperpile.com/pricing/

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