3 reference managers that will help you cite articles perfectly in your thesis


Tired of manually adding references to your document? Frustrated that you always seem to miss one or two articles in your Bibliography? Want to say goodbye to these problems forever? Say hello to reference managers! In this post, I will discuss three popular and free reference managers:


I will also share which of these three I personally use, and a handy table with an overview of these options to help you choose the one that is right for you. At the end of this post, I will also share a fourth option, Authorea, which may be of interest to you if you don’t want to bother using a separate reference manager.

Okay, but what is a reference manager?!

Not familiar with using a (separate) reference manager? Let’s start with a quick introduction!

What is a reference manager?

First things first: what does a reference manager do? Basically, a reference manager has two main purposes. Firstly, it’s a piece of software that allows you to build a database with all your references (and with some managers: a database of all your full-text articles in PDF). Usually, this database is stored in a separate file on your computer (but a reference database that is stored ‘in the cloud’ is also possible: see some of the options below). Secondly, a reference managers acts as a link between this database and your favorite word processor, such as Microsoft Word, OpenOffice or LyX. Whenever you want to cite an article from your database, the reference manager picks the correct reference and adds it to your document.

Why use a separate reference manager

You may say: “Isn’t something like this already built-in into most word processors, such as Microsoft Word? Why would I want to do this using a separate application?!”. Yes, you are right. But: there are some important downsides to using these ‘built-in’ referencing capabilities. For example, most word processors require you to manually enter each reference. This will cost you a lot of time, and is prone to errors (even when you copy-paste references from Google Scholar). But perhaps more importantly: it’s something that can easily be automated by a reference manager.

How it works

With a reference manager, adding a citation is (literally!) as easy as going to the web page of the journal where the article was published, and clicking on a button (in the reference manager, or in your web browser). The complete reference (article title, author names, journal title, publication data, number of pages, etc.) will automatically be added to your database. The only thing you have to do in your word processor is select the reference, and it will be included: in your text, and in your References-section. That’s right: two clicks and you’re done!

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What about reference styles?

A reference manager will also take care of the citation style for you, and it will apply it consistently in your document. For example: if your university requires you to use the APA or Harvard style of referencing, simply select this style in the reference manager and you’re done! Not happy with the style you have chosen? Simply pick another style, and the reference manager will automatically take care of the conversion to the new style for all your references.

Great! Is there more?

Last but not least, a reference manager will automatically build and update your References-section or so-called Bibliography. Whenever you add a new reference, the Bibliography will be updated with this new article, book or other academic source. Did you decide that you don’t need to cite an article after all? Simply remove the reference from your text, and the reference manager will also remove the reference from the Bibliography.

Reference managers


Zotero is a popular reference manager, best used in combination with Microsoft Word or Google Docs.1 It works as follows. Whenever you visit a webpage where an article is stored a button pops up (either in Zotero, or in your browser if you also downloaded the Zotero Connector plugin). Click the button, and both the article and the reference will automatically be stored in your Zotero database. Next, go to Microsoft Word, click the Zotero button and add your reference. It will automatically be added to your document, and to your Bibliography. Done!

Plus: cite ‘other’ content

A big plus about Zotero is that it’s not just good at storing academic references: it will also correctly reference other types of content.2 For example: when you go to the web page of the New York Times, Zotero will recognize that you are trying to cite a newspaper article, and it will store the reference as a ‘newspaper article’ (and not as a ‘web page’).

The Zotero interface. Source: Zotero website.
Sync references

Optionally, you can use the same reference database on multiple devices by syncing it via an online Zotero account.3 You get 300mb of space for free: if you need more, you will have to either buy more space or use a free online storage provider. For most students, 300mb will be plenty: this amounts to about 100-300 articles, more than enough for writing a thesis.


Note: I would like to stress that you do not have to register an account to use Zotero. An account is only necessary if you want to make use of the online storage, which will allow you to sync your database across multiple devices.

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Another popular and free reference manager is Mendeley.4 It is pretty much identical to Zotero (a quick overview of the main differences can be found here), so I will keep this discussion brief. Similar to Zotero, downloading references to your database is done from within your web browser by simply clicking a button. Inserting references into your document is also straightforward> download the right citation plugin for your word processors from the Mendeley website and you’re good to go!

An example of the interface of Mendeley.
Mendeley versus Zotero

A big difference with Zotero, however, is that you have to register an account before you can use Mendeley. All your references and articles are synced to your online account, which can host up to 2gb for free. That’s about 1,000 articles. A minor difference is the fact that Zotero links to your word processors automatically, whereas with Mendeley you have to install a separate plugin (although it will automatically select the correct plugin for you when you first start the program – a simple click will download and install it for you). Also note that Google Docs is not supported by Mendeley.

Mendeley signup
Illustration: Mendeley requires you to register an account before you can use their service.

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An example of the interface of JabRef.

JabRef is a completely open-source (free!) reference manager. JabRef only stores references: it does not store PDFs of the articles you request (something which Zotero and Mendeley both do).

The program connects to various popular citation databases, such as Google Scholar and Medline, and you can search these from within the program. If you are using FireFox as your web browser: there is an addon called JabFox that allows to you to add references to JabRef from within your browser, which arguably is even more convenient!

Jabref Scholar
An example of the built-in search capabilities of JabRef.
Word processor integrations of Jabref

Initially developed to export bibliographies for use with word processors that use LaTeX such as LyX, nowadays this reference manager also supports OpenOffice and LibreOffice, two popular open-source (free!) alternatives to Microsoft Word. Speaking of which: you can use JabRef with Microsoft Word, however, you will need to take some additional steps. Therefore, I can only wholeheartedly recommend this reference manager for:

  • people using a LaTeX word processor, such as LyX
  • people using OpenOffice or LibreOffice
Jabref OpenOffice
An example of the built-in OpenOffice referencing options of JabRef.
I frequently use Jabref (but it may not be for you…)

Personally, I have frequently used Jabref in combination with Lyx and the bibliography generator BibTeX (for an introduction of how to use JabRef with LyX click here). But obviously, it also works perfectly in combination with more modern bibliography generators such as BibLaTeX (for a short tutorial click here, or a LyX specific tutorial here).

LaTeX, LyX?

It’s possible that you have never heard of the terms LaTeX or LyX. LaTeX is a typesetting system, and LyX is a word processor that you can use in combination with the typesetting system: LaTeX! In short: they are an alternative to Microsoft Word for writing a dissertation. Curious to learn more about this option? I have written a blog post about LaTeX and LyX here.

Which one do I use?

Personally, I have been using Zotero since 2011. The fact that it allowed me to store articles to my own online database, which means that I am not limited to only using Zotero’s online storage, was the biggest plus for me (although for most students, that will not really be a concern). Furthermore, I have also come to like its intuitive interface, its ability to extract the correct reference by simply visiting a website (tip: always check that it did process the reference correctly in your database!), and its ability to easily connect to many different word processors: I have been using Zotero in combination with Microsoft Word, LibreOffice and LyX! This is why I personally advise students to go with Zotero. Nonetheless, if you feel that one of the other (good!) alternatives is more suited for you, go for it!

Which reference manager should you choose?

Options, options, options. Which one should you go for? Truth be told: your choice will largely depend on the writing tool that you will use. If you haven’t made a choice on this matter yet then I recommend you to also read my post on 4 popular word processor alternatives for academic writing.

If you have made up your mind, then the following table may help you choose the perfect reference manager to match your choice. Good luck! And just remember: there really is no wrong choice, just make sure you start using a reference manager !

Zotero Mendeley JabRef
Microsoft Word Yes Yes No
LibreOffice Writer Yes Yes Yes
Google Docs Yes No No
Lyx Best through Bibtex Best through Bibtex Best through Bibtex

Just one thing: I really don’t want to install a separate reference manager. What are my options?

Would you rather not bother with installing a separate reference manager on your computer? But would you still like to benefit from the capabilities of one? Then the online writing tool Authorea may be perfect for you! I discuss this option in the following post.

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