Zotero vs Mendeley

Why a thesis needs a reference manager at all

Many times a PhD thesis cites 150 to 300 sources. Scholars who type each reference by hand lose many days on that work. And small mistakes keep coming in. An author initial goes missing, or the year in the text differs from the list. Sometimes a paper cited in Chapter 2 is not there in the reference list at all.

In a reference manager you store each source one time, along with its PDF. Then you cite it from Word, and the software builds the reference list by itself in whatever style you have selected. Suppose late in the work your guide asks you to move to a different style, say between APA, IEEE or Harvard. You change only one setting, and all 300 entries change with it.

Some universities are now expecting it also. TNAU asks for a reference-management certificate at the time of thesis submission. Examiners also check the reference list early.

Zotero in practice

Zotero is free and open source software. You install two things, the desktop program and a connector for your browser. When you are on a journal page, Google Scholar or a publisher site, you click the connector once and the reference gets saved. Many times the PDF also comes with it.

The library is stored on your own computer, so Zotero works even without internet. This helps when the hostel Wi-Fi goes off. If you create a free zotero.org account, your library syncs between computers. Syncing of references has no limit. PDFs and other files take storage, and free storage is 300 MB only. Depending on the file size, that gets full at around a few hundred PDFs. For more space the paid plans are $20 a year for 2 GB, $60 for 6 GB and $120 for unlimited.

Plug-ins for Word, LibreOffice and Google Docs come along with Zotero and get installed by themselves. In Word you will see a Zotero tab with “Add/Edit Citation” and “Add/Edit Bibliography” buttons. Sometimes after a Word update the tab disappears. Then open Zotero’s settings, go under Cite → Word Processor Plugins, and reinstall the plug-in from there.

Mendeley in practice

Mendeley is owned by Elsevier. For many years scholars used Mendeley Desktop, and a Word plug-in came along with it. From 1 September 2022, Mendeley Desktop was removed from download. Those who had it installed already could continue to sign in, but Elsevier said it will stop Desktop sign-ins later and give notice before that. New users are given Mendeley Reference Manager.

For Reference Manager the Word add-in is Mendeley Cite. You install it from Microsoft AppSource. It works with Microsoft 365, Word 2016 and later versions, and Word on iPad. If the college computer has an older Word, Mendeley Cite will not work there. Several university libraries are also saying that Mendeley Cite does not work in Google Docs.

Where Mendeley scores over Zotero is the storage. Free account comes with 2 GB, so it can keep many more PDFs than the free 300 MB of Zotero. It is also built around the online library, which suits you if you keep moving between a lab computer and a laptop.

Which one should you choose?

We usually go by the scholar’s own situation.

• If you write in Google Docs or LibreOffice, or the Word on your college computer is old, take Zotero.
• When you have thousands of PDFs and don’t want to pay for storage, Mendeley’s 2 GB is useful. Another way is to use Zotero and keep the PDFs on your own drive, which Zotero allows.
• Sometimes the supervisor or the lab shares a Mendeley group and wants all members in it. Then stay with the lab and learn Mendeley Cite properly.
• Your Mendeley Desktop setup is working and the thesis is almost finished. In that case don’t change anything now. Complete the thesis first.

Both tools use the same open library of citation styles, called Citation Style Language, and it has more than 10,000 styles. So the choice of tool will not limit which citation style you can use.

Switching from Mendeley to Zotero without breaking your thesis

Moving the library is not difficult. First sync Mendeley, so all your files are on its servers. Then in Zotero go to File → Import and select the online import from Mendeley Reference Manager. Zotero brings over your data with the full folder structure.

The difficult part is your Word files. Zotero can read citations made with the old Mendeley Desktop plug-in, and it relinks them to the imported items. Citations put in with Mendeley Cite are different, and Zotero cannot read those. Chapters cited through Mendeley Cite will need every citation put in again from Zotero, one by one.

Take a backup copy of all chapters before you switch. Do the change in one chapter alone, then check the reference list against the citations in that chapter. Do the remaining chapters only after that.

Mistakes that cost scholars a week at the end

Believing the imported data fully. A reference saved from a web page may come with the journal name in capitals, no issue number, or the author name in the wrong order. Check every entry once at the time of saving itself, not in the night before submission.

Typing over the reference list. When you correct the bibliography by hand in Word, the next refresh removes your correction. Make the correction in the library instead.

Converting to plain text too early. Many universities want the final file without live fields. Do this conversion at the very end, on a copy, and keep the live version.

Mixing two tools in one document. Zotero citations and Mendeley citations cannot understand each other. Use one tool only for one thesis.

Forgetting page numbers for quotes. In most styles an exact quotation needs the page number. Without it, defending a match in the similarity report also become harder. For that part, read our guide on reducing similarity.

When the references still look wrong

Sometimes the problem is in the style itself. Your university may ask for an author-date format which is close to APA but not exactly APA, and no ready style matches it. Anna University is one example. Its regulations ask for author-year citations, and your own papers have to come in a separate list, not inside the reference list.

Then take the closest style and correct the few differences at the end, on a copy. What to check is listed in our formatting checklist. If you want to give the layout work to someone, our thesis formatting service can set up the reference list as per your university format, using your own library. Need only one reference in a hurry? Paste the DOI in our citation generator and it gives a formatted entry.