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Which reference manager?: Comparison of EndNote, Mendeley and Zotero

This guide is intended to help you choose a right reference management tool for your study and research.

Reference management tools

A reference management tool is a software for storing and managing information resources. Generally, a reference management tool can help you:

  • import references from search engines, databases and websites 
  • save PDFs, images and other documents
  • annotate PDFs
  • insert citations and create bibliographies on Word documents  
  • collaborate with other researchers

EndNote, Mendeley and Zotero are the most popular reference management tools used by many researchers and students.

Find more details about these three tools in the following comparison table and detailed instructions in our online guides for each tool.

EndNote, Mendeley and Zotero: which is the best tool for you

The following comparison table of EndNote, Mendeley and Zotero may help you choose a right tool to meet your research needs.

Software support
  • AUT Library supports the use of EndNote (online guide, workshops and consultations)
  • Software support is provided by AUT ICT Services
  • EndNote website provides online training materials and a blog 
  • AUT Library online guide
  • Mendeley website provides online training materials/blog
  • AUT Library online guide
  • Zotero website provides training materials and discussion forums/ blog
  • Available in all AUT computers
  • AUT users can download a free copy from the AUT website to a personal computer
  • Free
  • AUT Institutional membership provides additional data storage
  • Free 
  • Pay for extra online storage
Operating systems
  • Windows 7, 8, 8.1, 10
  • MacOS 10.14 or later

Check the EndNote website for more details and latest updates.

  • Windows 7, 8.1, 10 

  • MacOS 10.10, or later
  • Linux

Check the Mendeley website for more details and latest updates.

  • Windows 7 or later
  • MacOS 11 or later
  • Linux

Check the Zotero website for more details and latest updates.


Online versions
  • Desktop
  • Online - EndNote Online
  • Free iPad app
  • Sync between devices and online library
  • Desktop
  • Online - Mendeley Reference Manager
  • Sync between devices and online library
  • Desktop
  • Online
  • Sync between devices and online library
  • Unlimited local storage
  • 2GB online storage 
  • AUT users: 100 GB personal & shared storage
  • Free account: 2GB storage
  • Unlimited local storage
  • 300MB free online storage
Work with Word processor
  • Desktop: MS Word, OpenOffice
  • EndNote cite while you write (CWYW) is a  comprehensive tool for citing references and editing citations
  • CWYW for both desktop and online libraries
  • A better tool for managing long documents and a large reference collection
  • MS Word, OpenOffice
  • Cite while you write with desktop library
  • MS Word, LibreOffice, Google Docs
  • Cite while you write with desktop library
Add references
  • Direct export references from databases
  • Drag and drop PDFs to EndNote with reference data
  • Add references manually
  • Capture online resources to EndNote Online
  • "Find reference updates" function
  • Export references from some databases
  • Drag and drop PDFs to Mendeley with reference data
  • Use web Importer to get references from databases/websites instantly
  • Add references directly from Mendeley website
  • Add references manually
  • Export references from databases
  • It is easier to use Zotero to collect references from websites.
  • PDFs can be downloaded along with reference data
  • Add references manually
  • Snapshots of webpages are also saved with references
Save PDFs
  • Import PDFs or PDF folders
  • Import PDF folders automatically
  • Drag and drop PDFs
  • Use "Find full-text" to download PDFs with a DOI number
  • PDF annotation
  • Import PDFs using a Web importer
  • Drag and drop PDFs
  • Import PDF folders automatically
  • PDF annotation in a Notebook
  • Use browser connector to collect references from websites. PDFs are sometimes downloaded along with reference data
  • Drag and drop PDFs/PDF folders to Zotero
Edit output styles
  • Easy to edit output styles
  • Use the CSL editor 
  • Use the CSL Visual Editor
Share & collaborate
  • EndNote desktop library, including references, PDFs and annotation, can be shared with 100 people. 
  • EndNote Online - share groups of references
  • AUT account: share references, PDFs and annotations with up to 100 people
  • Free account: share groups with up to 25 people
  • Share citations and documents with others using your online account
  • As the size of a free Zotero account is only up to 300MB, sharing a large number of references/PDFs may need to pay for an extra data storage