Overview
The three most widely used academic reference managers have each changed recently. Zotero is free and open source; Zotero 8 arrived in January 2026 with a redesigned citation dialog, and Zotero 9 followed within months as the project moved to a faster release cycle. Mendeley's current application is Mendeley Reference Manager with the Mendeley Cite add-in for Word; the older Mendeley Desktop can no longer be downloaded for new installations and receives maintenance only, so we recommend migrating. EndNote's current desktop version is EndNote 2025, with Cite While You Write for Word and EndNote Web for sync.
We start with your situation: which tool your institution supports or licenses, whether you collaborate with co-authors who use a particular tool, whether you write in Word, Google Docs or LaTeX, and which citation style you need. Then we install or configure the software and plugin, set the citation style (including a specific edition or institutional Harvard variant), and fix the library records that produce formatting errors.
Sessions are live and hands-on, on your own computer and library, so you learn by doing. You leave with a working setup, a clean library and a short written workflow for capturing, organizing, citing and backing up sources.
Who it’s for and the problems it solves
This is for you if you are…
- Students starting a dissertation or thesis who want to set up referencing properly from the start
- Doctoral candidates with a large, messy library built up over years
- Researchers still on Mendeley Desktop or an old EndNote version who need to migrate
- Research teams who want a shared group library for a project or review
- Writers switching between Word, Google Docs and LaTeX workflows
Common problems we help with
- The Word plugin tab disappeared or citations will not update
- Your library has duplicates, all-caps titles and incorrect item types
- You need a specific style (such as Cite Them Right Harvard or OSCOLA) and cannot find or install it
- You are still using Mendeley Desktop and are unsure how to move to Mendeley Reference Manager
- Co-authors use different tools and citations break when you exchange files
What’s included — and what isn’t
Included
- Advice on choosing Zotero, Mendeley Reference Manager or EndNote for your circumstances
- Installation and configuration of the desktop app, browser connector and Word or Google Docs plugin
- Installing and selecting the correct citation style (CSL styles for Zotero and Mendeley, output styles for EndNote), including edition-specific and institutional styles
- Library cleanup: duplicate merging, item-type corrections, title case, author name fixes, missing DOIs and PDFs attached
- Migration between tools or from Mendeley Desktop to Mendeley Reference Manager, with checks that nothing was lost
- Collections, tags and naming conventions that suit a thesis, systematic review or multi-paper project
- Group libraries and sharing for co-authors
- BibTeX or biblatex export for LaTeX and Overleaf users (for example via Zotero's Better BibTeX plugin)
- Backup and sync setup, and a written workflow for future use
Not included
- Purchasing or licensing software (EndNote is paid; your institution may provide it)
- Literature searching or selecting sources for you
- Reading or summarizing papers in your library
- Fixing citation formatting in a finished document (see citation and referencing check)
What you receive
- Configured setup
- Reference manager, browser connector and word-processor plugin installed and tested with your citation style.
- Cleaned library
- Duplicates merged, item types and key fields corrected, and a short report of what changed.
- Workflow guide
- A one- to two-page guide tailored to your tool, style and writing software: capture, organize, cite, back up.
- Recorded session
- A recording of the live session, on request, for later reference.
How it works
Needs check
You tell us your tool (or none yet), writing software, style, library size and any institutional licensing. We recommend an approach.
Setup session
In a live screen-share, we install or update the software and plugin and set the citation style together.
Library cleanup
We clean the library with you, or offline with a copy of your library if you prefer.
Workflow practice
You insert citations and a bibliography in a test document and practice the steps you will use daily.
Follow-up
A short follow-up to answer questions once you have used the setup in real writing.
Tools and features we set up
- Zotero
- Free and open source, with Zotero Connector for browsers and plugins for Word, LibreOffice and Google Docs. Zotero 8 (January 2026) redesigned the citation dialog; Zotero 9 followed with further updates. Uses CSL styles.
- Mendeley Reference Manager
- Elsevier's current Mendeley application with the Mendeley Cite add-in for Word. Mendeley Desktop is no longer available for new downloads and receives maintenance only, so migration is advisable.
- EndNote 2025
- Clarivate's paid reference manager with Cite While You Write for Word, EndNote Web sync, and a large library of output styles. Common in institutions that license it.
- Citation Style Language (CSL)
- The open style format used by Zotero and Mendeley; thousands of journal and institutional styles are available, and styles can be adapted.
- Better BibTeX
- A Zotero plugin that maintains stable citation keys and auto-exports .bib files for LaTeX and Overleaf.
- Deduplication and metadata retrieval
- Built-in duplicate detection, DOI-based metadata lookup, and retrieval of open-access PDFs where available.
Which reference manager should you use?
There is no single best tool; the right choice depends on your situation. Zotero suits most individual researchers, especially those who want free, flexible software with strong LaTeX support and many community plugins. EndNote suits those whose institution licenses it, who work with teams already on EndNote, or who handle very large libraries in fields where it is standard. Mendeley Reference Manager suits users already in the Mendeley ecosystem who want simple PDF reading and annotation.
Switching is possible, but in-document citations do not always transfer cleanly between tools. If you are midway through a thesis, it is often better to stay with your current tool and clean it up than to switch.
- Institutional license and support available locally
- Co-authors' tools, if you write together
- Writing environment: Word, Google Docs, LaTeX/Overleaf
- Need for a specific style or edition, such as OSCOLA 5th edition or Cite Them Right 13th edition
- Library size and PDF annotation habits
Library hygiene: the fix that lasts
Most formatting errors in bibliographies start in the library. A journal article imported as a web page, a title stored in all capitals, an organization entered as a person, or a missing DOI will produce the same error in every document. Cleaning the library once — and learning to check new entries at the point of capture — saves hours at every submission.
If you need a finished document checked as well, our citation and referencing check works well after setup.
Moving from Mendeley Desktop
Mendeley Desktop remains installed for many long-time users, but Elsevier now focuses development on Mendeley Reference Manager and Mendeley Cite, and Desktop cannot be newly downloaded. Documents written with the old Desktop Word plugin use a different citation format, so older theses and papers need care when moving to Mendeley Cite. We check your library syncs completely, test citations in an existing document, and plan the move around your writing schedule.
What the work can look like
Illustrative example — fictional data
Migrating a doctoral library from Mendeley Desktop to Zotero
An illustrative doctoral candidate (fictional) in education has 1,150 references in Mendeley Desktop, writes in Word, and needs APA 7. Their co-authors use Zotero, and the old Word plugin has stopped working after a Word update.
Decision
Because co-authors used Zotero and the candidate wanted better LaTeX support for a future paper, we agreed a move to Zotero rather than to Mendeley Reference Manager.
Migration and cleanup
The library was imported with PDFs and annotations. Deduplication merged 86 duplicates; 140 titles in all capitals were corrected; 37 reports mistakenly saved as journal articles were retyped.
Workflow
The candidate practiced inserting citations with the new citation dialog, set up a group library with co-authors, and received a one-page guide for capture and backup.
Fictional, illustrative scenario. Numbers are invented to show the type of work involved.
What you’ll need to provide
- Access to your computer via screen-share during sessions, with administrator rights to install software
- Your existing library or export file (RIS, BibTeX, EndNote XML) if you have one
- Required citation style and edition, and your institution's style guide
- Your writing software and version (Word for Windows or Mac, Google Docs, Overleaf)
- Any institutional licensing details for EndNote
You don’t need everything ready to ask for a quote — tell us what you have and we’ll say what’s missing.
What affects price and turnaround
Price depends on
- Number and length of live sessions
- Library size and how much cleanup it needs
- Migration between tools, or from Mendeley Desktop
- Group library setup for several users
- LaTeX integration or custom style adaptation
Turnaround depends on
- Scheduling of live sessions across time zones
- Library size for offline cleanup
- Whether software installation requires IT approval at your institution
Every project is quoted individually. How we price our work.
Questions people ask before starting
Is Mendeley Desktop still usable?
Existing installations may still work, and Elsevier has said it receives essential maintenance, but new downloads are not offered and new features go into Mendeley Reference Manager. We recommend planning a migration, especially before a major deadline.
Which is better, Zotero or EndNote?
Both are capable. Zotero is free and flexible; EndNote is common where institutions license it. We help you choose based on your license, collaborators and writing software.
Can I switch tools in the middle of my thesis?
Yes, but citations already inserted in Word may need re-linking. We assess the effort first and sometimes recommend cleaning up your current tool instead.
Do you need access to my computer?
For live setup, yes, via screen-share with your permission. You stay in control, and we can also work on an exported copy of your library instead.
Can you set up my university's own Harvard style?
Often an official CSL or EndNote style already exists. If not, we can adapt the closest style and test it against your guide's examples.
Does this work with Google Docs or Overleaf?
Zotero integrates with Google Docs; Overleaf can link to Zotero and Mendeley libraries or use an exported .bib file. We configure the option that fits your workflow.