Mendeley vs Zotero: Which Is Best For Citation Management?

Choosing a citation management tool can be overwhelming, particularly when deciding between Mendeley and Zotero. Each offers unique features tailored to enhance academic research and organisation.

This article delves into the core differences between Mendeley and Zotero, examining aspects from storage and file management to user interface and collaboration features. 

Our goal is to help you determine which tool best aligns with your research needs and collaborative style, making your citation management more efficient and tailored.

Mendeley vs Zotero

Storage Options2GB free cloud storage.300MB free, expandable with any WebDAV server.
File ManagementIntegrated PDF reader for annotations.Organizes PDFs, needs extra software for deep editing.
Citation Styles and FlexibilitySupports many styles but with limited customization.Supports many styles with easy customization.
User Interface and ExperienceSleek and user-friendly.Utilitarian with flexible organization options.
Collaboration FeaturesPrivate groups up to 25 members.Unlimited public or private groups.

What Is Mendeley?

Mendeley is a standout reference and citation management system that helps you to: 

  • organize your research,
  • manage citations, and 
  • share insights with colleagues 

Using Mendeley, you can import PDF files from your desktop or directly from the web. This is complemented by plugins for web browsers that enable a single-click capture of research papers and their metadata into your personal library.

One feature you will appreciate is the ability to cite directly from Mendeley into your word processor. It also automatically adapting to the citation style you choose—whether APA, MLA, or any of the thousands available.

For collaborative projects, Mendeley allows you to share citations and documents within a private group or invite-only public group, supporting up to 25 members for free. This makes it incredibly easy to manage joint research efforts. 

What Is Zotero?

Zotero stands out as a free, open-source reference manager that simplifies the lives of researchers like you by managing bibliographies and citations in research papers.

One of Zotero’s most lauded features is its ability to seamlessly capture citations from the web with its browser extension. 

You will also find Zotero incredibly helpful for organizing research material thanks to its powerful tagging and searching capabilities.

These allow you to easily find any piece of work, whether it’s a PDF file or a web link. Zotero syncs all your data across devices, making your database accessible wherever you are.

Zotero also supports group libraries, enabling you to collaborate and share research materials and citations with peers.

Mendeley vs Zotero: What Are The Differences?

While both Mendeley and Zotero offer robust solutions in organising your research, they come in slightly different flavors. Here are some ways they are different from each other.

Storage Options

Mendeley offers you 2GB of free cloud storage. This might sound generous until you see Zotero’s approach: it starts you off with 300MB of free cloud storage but doesn’t limit you to its own cloud.

Zotero allows you to sync your data with any WebDAV server, providing flexibility if you need more space.

This can be particularly useful if your research involves a lot of large files and you are comfortable managing your own data backups.

File Management

Mendeley stands out with its integrated PDF reader. This allows you to annotate and highlight PDFs directly within the app.

If you spend a lot of time reviewing journal articles, this feature turns Mendeley into not just a citation tool but a comprehensive review platform. 

Zotero’s PDF handling is more about organization than annotation. It does allow PDF indexing for easy searchability within the app, but for in-depth PDF editing, you would need to use another program.

Citation Styles and Flexibility

Both tools support thousands of citation styles, from APA to lesser-known types tailored to specific academic journals.

However, Zotero takes the lead in how easily you can switch between styles and even customize them.

Thanks to its active community forums and open-source nature, it may be easier to work on your citations in Mendeley, be it to:

  • finding,
  • edit, or
  • refining.

This openness can be a significant advantage if your field requires a highly specific citation format that isn’t mainstream.

User Interface and Experience

Mendeley’s interface is often praised for its sleekness and ease of use, particularly in how it integrates document management directly into the citation process.

There’s also support for many devices, such as Mendeley Desktop.

The newly designed Mendeley Reference Manager simplifies how you interact with your library and annotations. Zotero’s interface, while highly functional, can feel a bit more utilitarian.

The trade-off is that Zotero offers more flexibility in organizing your research materials through its tagging and folder systems.

Collaboration Features

Both platforms allow you to share your research with others, which is essential for collaborative projects.

Mendeley limits you to creating private groups with up to 25 members, which might be sufficient for most projects but could be restrictive for larger collaborative efforts.

Zotero, in contrast, lets you create unlimited public or private groups, which is a boon if you’re working in large teams or need to manage multiple projects with different groups of colleagues.

How To Choose Between Mendeley and Zotero?

Deciding between Zotero and Mendeley for managing your research can feel daunting.

Both tools come highly recommended, but each has distinct features that may suit different research needs. Here’s how you can choose the right one for you.

How Frequently Do You Work With PDFs?

If you frequently work with PDFs, you might lean towards Mendeley. It has an integrated PDF viewer that lets you annotate and highlight documents directly within the application.

This is immensely helpful if you’re someone who likes to add notes and insights directly onto your research materials.

Plus, Mendeley’s 2GB of free cloud storage means you can sync your annotated files across all your devices without fuss.

How Broad Are Your Resource Types?

On the other hand, if your work involves a broad array of source types or you require more flexible storage options, consider to use Zotero instead.

Zotero is open source and supports a wide variety of reference types and metadata from webpages, which is perfect if your research pulls from diverse resources.

Additionally, Zotero’s capability to sync with any WebDAV server gives you more control over where and how your data is stored.

Do You Need Collaboration Features?

Collaboration features also differ significantly between the two.

\Mendeley allows you to create private groups with up to 25 members—sufficient for most projects but limiting for larger teams.

Zotero, meanwhile, offers the ability to create unlimited public and private groups, which is invaluable for large-scale research projects involving many collaborators.

Do You Need Community Support & Customisation?

For those who value community support and the flexibility to customize tools, Zotero’s strong community platform and forums are a treasure trove of tips, tricks, and custom citation styles.

In many cases, you may find Zotero easier to be adjusted to your specific needs, compared to Mendeley.

Are There Alternatives to Mendeley And Zotero?

Mendeley and Zotero are not the only citation management systems out there, which means you can find alternatives if you want to use something else.


EndNote is particularly well-suited for those deep in complex research. It’s more than a citation manager; it integrates with Microsoft Word to create bibliographies and manage references as you write.

EndNote stands out with its ability to handle a large number of citation styles and its robust database syncing capabilities. This ensures your library is always up-to-date across all your devices.

ReadCube Papers

ReadCube Papers is a newer player that has quickly gained traction due to its modern interface and powerful features. It excels in manuscript matching, helping you find the best journal for your research.

Like Mendeley, it allows PDF annotations directly in the app and offers excellent support for importing PDF metadata, streamlining how you organize your articles.


Citavi is unique because it not only manages citations but also aids in knowledge organization. You can annotate PDFs, save quotations, and create task lists directly in the app.

Citavi’s project management features are a boon if you’re juggling multiple research projects, allowing you to track progress in one place.

Mendeley vs Zotero Citation Manager Comparison

Choosing between Mendeley and Zotero for citation management boils down to your specific needs. Mendeley is ideal if you value a sleek interface and integrated PDF annotations, suitable for solo projects or small teams.

Zotero excels in flexible storage options, extensive customization, and is better suited for large-scale collaborations due to its capability to handle unlimited groups.

Evaluate your primary requirements in research management to make the best choice between these two robust tools.

The Author

Dr Andrew Stapleton has a Masters and PhD in Chemistry from the UK and Australia. He has many years of research experience and has worked as a Postdoctoral Fellow and Associate at a number of Universities. Although having secured funding for his own research, he left academia to help others with his YouTube channel all about the inner workings of academia and how to make it work for you.