20 October 2026 · By Thesisroom

Mendeley vs Zotero: Which Reference Manager Fits Your Thesis

Mendeley and Zotero compared on what they cost, where they cite, storage, Mendeley Desktop's status, retraction flags, and how to switch mid-thesis safely.

Mendeley vs Zotero comes down to where you write and how much you want to depend on one company. Choose Zotero if you want a free, open-source library that cites in Word, LibreOffice and Google Docs and flags retracted papers. Choose Mendeley if you cite only in Word, including Word on an iPad, and want highlights from many PDFs gathered in one notebook.

Both apps are free to use. The biggest practical difference between Zotero and Mendeley on 18 October 2026 is how clearly each one tells you what you get. Zotero publishes its storage amounts and prices. Mendeley's public pages that we could open did not state a storage amount, and its pricing page would not load for us.

Mendeley vs Zotero at a glance

Both are free reference managers that save sources from your browser and build citations in your word processor. They differ most in who makes them, which word processors they support and how open they are about storage. Every row below comes from the makers' own pages, linked in the sections that follow.

	Zotero	Mendeley
Who makes it	The Corporation for Digital Scholarship, a nonprofit	Elsevier
Cost of the app	Free and open source	Free
Desktop	Windows 10 or newer, macOS 10.15 or newer, Linux	Mendeley Reference Manager on Windows, Mac and Linux, plus a web library
Mobile	Official iOS and Android apps	Mendeley Cite runs in Word for iPad
Word processors	Word (Windows and Mac), LibreOffice, Google Docs	Word (Office 365 and Word 2016 or later) through Mendeley Cite
Saving from the web	Zotero Connector for Chrome, Firefox, Edge and Safari	Mendeley Web Importer
Free file storage	300 MB	Not stated on the pages we could open
Paid storage	2 GB for $20 a year, 6 GB for $60 a year, unlimited for $120 a year	Pricing page would not load for us
Shared libraries	Groups with no member limit	Shared libraries for groups
Retracted papers	Flags retracted items that have a DOI or PMID	Not described on the pages we opened

What Zotero does well

Zotero is free, open source and run by a nonprofit. Its about page says it is a project of the Corporation for Digital Scholarship and was created at the Roy Rosenzweig Center for History and New Media at George Mason University.

It covers more word processors. Zotero's word processor integration page says the Word and LibreOffice plugins are bundled with Zotero. Its system requirements page lists Word 2010 to 2024 or Office 365 on Windows, Word 2016 to 2024 or Office 365 on Mac, and LibreOffice 5.2 or later. Zotero's Google Docs support comes through the Zotero Connector and works locally on your computer.

There is one catch worth knowing before you write a long thesis in Google Docs. Zotero's own page says that with more than 100 citations, a single citation update can take up to 10 seconds. If your thesis will carry hundreds of references, Word or LibreOffice may feel faster.

Zotero also watches for retractions. In its 2019 announcement, Zotero said it flags retracted items in your library using Retraction Watch data and warns you before you cite one in your word processor. The same post says the feature only works for items with a DOI or PMID.

Syncing your library data costs nothing. Zotero's sync documentation says data syncing is free and unlimited, and it is separate from syncing attached files such as PDFs.

Zotero also reaches more devices and more people. Its mobile page lists official apps for iOS and Android. Its groups page says there is no limit on how many members can join a group.

What Mendeley does well

Mendeley is free and backed by a large publisher. Elsevier's Mendeley product page describes it as "a free reference manager" that can store, organise, share and cite references. The Mendeley homepage says it works on Windows, Mac, Linux and all browsers.

Its strongest feature for reading is Mendeley Notebook. The Mendeley Reference Manager page says Notebook gathers your highlights and notes from several PDFs in one place. That suits a literature review where you compare passages across papers.

Mendeley Cite is a Word add-in. Its Mendeley Cite page says it works with Office 365, Word 2016 and later, and the Word app for iPad. Mendeley's blog also describes a Watched Folder feature in the desktop Reference Manager. Drop a file into that folder and Mendeley adds it to your library.

Saving and sharing are covered too. A July 2026 Mendeley post says the Web Importer spots article identifiers on a web page and saves the details, plus the full text where available. A November 2025 post suggests setting up shared libraries with your team.

Mendeley has added AI reading features. Its January 2026 blog post names Reading Assistant, Ask My Library and Compare Experiments. The post links these features to Mendeley's pricing page, which we could not open on 18 October 2026, so check the cost there before you count on them.

Zotero vs Mendeley on storage

Zotero gives every user 300 MB of free file storage and sells more. Its storage page lists 2 GB for $20 a year, 6 GB for $60 a year and unlimited storage for $120 a year. Zotero's sync documentation says you can sync files through a WebDAV server instead, and your institution may be able to provide one.

For Mendeley, we could not confirm a current storage figure on any Mendeley or Elsevier page we could open. Some guides, including older posts on this blog, give a figure, but we have left it out because we could not check it today. If storage decides your choice, log in to Mendeley and check your account before you move a large PDF collection.

The storage question has its own guide. Zotero storage options for students covers WebDAV, institutional plans, linked files and how to stay inside the free 300 MB.

Is Mendeley Desktop still available

Yes, though it is no longer being developed. Mendeley had announced that Mendeley Desktop would stop being available for new downloads. Then, in a July 2025 post titled "Mendeley Desktop is Here to Stay", it said Desktop would stay, with a download link to version 1.19.8.

The same post says there will be no new features for Desktop, though Mendeley will keep fixing critical security issues. Future updates go to Mendeley Reference Manager. If you still use Desktop, sync your library to the cloud before you sign in to Reference Manager, as that post advises.

Older Word versions are a reason some people stay on Desktop. The Mendeley Cite page points users of earlier Word versions to the citation plugin that comes with Mendeley Desktop.

Zotero or Mendeley: which is better for your thesis

Neither is better for everyone, but a few facts decide it quickly. Work down this list and stop at the first line that matches you.

You write in Google Docs or LibreOffice. Choose Zotero. The Mendeley pages we opened describe Mendeley Cite for Word only.
Your supervisor or lab already shares a library in one of them. Join that one. Shared libraries only help if everyone uses the same tool.
You have years of citations in Word documents made with Mendeley Cite. Think hard before switching. Zotero says citations created with Mendeley Cite are not readable by Zotero, so you would re-insert them.
You cite in Word on an iPad. Mendeley Cite says it supports the Word app for iPad. Zotero's system requirements page does not list it.
You want your references to sit with a nonprofit, open-source project. Choose Zotero.
You want warnings when a paper you saved is retracted. Zotero does this for items with a DOI or PMID. Either way, check retractions yourself before submission.

Switching from Mendeley to Zotero without breaking your citations

You can move a Mendeley library into Zotero, but your Word documents need more care than the library. Follow these steps in order, based on Zotero's Mendeley import guide.

Sync everything to Mendeley first. Zotero imports from your online Mendeley library, so make sure all your data and files have synced to Mendeley's servers.
Update Zotero. Use Help, then "Check for Updates".
Run the import. In Zotero, choose File, then Import, then "Mendeley Reference Manager (online import)", and log in when asked. Zotero says it never sees or stores your Mendeley password.
Move group items by hand. Zotero cannot import Mendeley group libraries directly. Copy group items into a collection in your own Mendeley library first.
Check your login type. If you sign in to Mendeley through your institution, you may need a separate personal Mendeley account linked to it.
Save a copy of every thesis document before you touch it. Zotero's Word and LibreOffice plugins can relink citations made with Mendeley Desktop. Citations made with Mendeley Cite cannot be read, so plan to re-insert those.
Spot-check before you trust it. Open a sample of imported items, for example one from each folder. Confirm the authors, year and attached PDF came across.

A simple rule for timing: switch between pieces of writing, not in the middle of one. Finishing a section in the tool that made its citations saves you a second round of re-inserting them.

Check the references themselves, whichever you pick

A reference manager formats what you saved, so a wrong year or a misspelt author in the saved entry carries straight into your thesis. Zotero's retraction flag only covers items with a DOI or PMID, so anything without one needs a manual check. Before submission, open each DOI link and compare the title, authors and year with your entry.

If your library has grown messy, our guide to organising sources for a PhD shows how to group sources by the section they support, using Zotero folders or Mendeley collections. For a wider list of tools, including Paperpile and EndNote, see our Zotero alternatives guide.

What Thesisroom does with this

Thesisroom is not a reference manager, and it works with a reference list from either one. Thesisroom's Citation Check looks each reference up in eight registries: Crossref, OpenAlex, Semantic Scholar, PubMed, Retraction Watch, DOAJ, CORE and Unpaywall. It shows which references it could verify, which are retracted and which need checking by hand.

To try the idea without an account, paste a bibliography exported from Zotero or Mendeley into the free citation checker. It uses a smaller set of registries than Citation Check, so treat it as a first pass.

Frequently asked questions

Is Mendeley or Zotero better for a PhD?

Neither wins for everyone. Zotero suits you if you write in Google Docs or LibreOffice or want a nonprofit, open-source tool. Mendeley suits you if you cite only in Word, including on an iPad, and like gathering PDF highlights in one notebook. If your lab shares a library, use theirs.

Is Zotero completely free?

The Zotero app is free and open source, and syncing your library data is free and unlimited. File storage for PDFs is free up to 300 MB. Beyond that, Zotero sells 2 GB for $20 a year, 6 GB for $60 a year and unlimited storage for $120 a year, or you can use your own WebDAV server.

Is Mendeley still free?

Elsevier describes Mendeley as a free reference manager. Mendeley's newer AI reading features are linked from its blog to a pricing page, which we could not open on 18 October 2026. Check that page before relying on those features.

Can I use Zotero and Mendeley at the same time?

You can keep both libraries, and Zotero can import a Mendeley library. Avoid mixing them inside one thesis document. Zotero says it cannot read citations created with Mendeley Cite, so a mixed document is hard to keep consistent.

Does Zotero check for retracted papers?

Yes, for items with a DOI or PMID. Zotero announced in 2019 that it flags retracted items in your library using Retraction Watch data and warns you before you cite one. Items without a DOI or PMID are not covered, so check those by hand.

Can I move my Mendeley library into Zotero?

Yes. Sync your Mendeley library online, update Zotero, then choose File, Import and the Mendeley online import option. Group libraries do not import directly, and citations made with Mendeley Cite in Word cannot be read by Zotero.

Sources

How this guide was made: Thesisroom drafted this guide with the help of AI writing tools, then checked every fact, figure and source by hand against the references linked above.