Zotero, Mendeley and the alternatives: an honest comparison for researchers
What Zotero, Mendeley, EndNote, Paperpile, JabRef and ScholarThread are each best at, where they overlap, and how to choose, including when you should not switch.
Short answer: for most researchers, Zotero is the right reference manager: it is free, open source and has citation plugins for the main word processors. Choose EndNote if your institution provides it and your group already uses it, Paperpile if you write in Google Docs, and JabRef if you live in LaTeX and .bib files. ScholarThread is not a replacement for a citation plugin. It is where you read, annotate, take notes and ask questions across your papers, and it works with a Zotero library or on its own.
We make ScholarThread, so read this with that in mind. We have tried to say plainly where other tools are the better choice.
Two different jobs
Researchers often look for "a better Zotero" when what they want is help with a different job.
- Managing references and citing them: collecting papers, keeping their metadata clean, and inserting citations and a bibliography while you write. This is what Zotero, Mendeley, EndNote, Paperpile and JabRef are for.
- Reading and thinking with them: reading closely, annotating, writing notes that link back to the source, and finding connections and disagreements across papers. Reference managers do some of this; it is the main job of ScholarThread, and of note apps such as Obsidian.
If your frustration is with citing, switch reference manager, or do not switch at all. If it is with reading and notes, add a tool rather than replacing your library.
At a glance
| Tool | Best for | Cost | Platforms | Keep in mind |
|---|---|---|---|---|
| Zotero | Collecting, organising and citing in Word, LibreOffice and Google Docs | Free and open source; extra cloud storage is paid | Windows, macOS, Linux, iPhone, iPad, web library | Run by a non-profit with a large plugin ecosystem |
| Mendeley | A free reference manager with a Word citation plugin | Free | Desktop app and web | Owned by Elsevier, which matters to some researchers |
| EndNote | Large libraries and institutions that already license it | Paid licence, often provided by universities | Windows, macOS, web | Expensive if your institution does not provide it |
| Paperpile | Writing in Google Docs, working in the browser | Subscription | Browser-based | Built around Google's ecosystem |
| JabRef | LaTeX users who manage .bib files directly | Free and open source | Windows, macOS, Linux | BibTeX-centred by design |
| ScholarThread | Reading, annotating, linked notes and questions answered from your own papers | Free plan; Pro subscription with an academic price | Web, iPhone, iPad; Android in development | No word-processor citation plugin; launched in 2026 |
Checked on 27 October 2026. Prices and features change, so confirm on each tool's own site before you decide.
How to choose
- You are starting a PhD and have no system yet: start with Zotero. It is free, widely supported by university libraries, and its library exports to every other tool here.
- Your supervisor or group shares an EndNote library: stay with EndNote for citing, so you can collaborate.
- You write mostly in Google Docs: look at Paperpile.
- You write in LaTeX: Zotero with a BibTeX export, or JabRef if you prefer to edit
.bibfiles directly. - Your references are fine, but reading and notes are scattered across PDFs, folders and apps: keep your reference manager and add a reading and notes tool on top. That is where ScholarThread for Zotero users fits.
- You want to ask questions of your own papers and check every answer against the source: see AI that answers from your own papers.
Where note apps and AI tools fit
- Obsidian, Notion and Logseq are note apps. They are excellent for writing, but they do not manage references or read PDFs on their own, so researchers usually connect them to a reference manager. ScholarThread exports notes as an Obsidian-compatible Markdown vault and can sync them with a Git repository, so you can keep using Obsidian.
- Elicit and SciSpace search and summarise the wider literature. They help you find papers; they are not where you keep and annotate the ones you have read.
- NotebookLM answers questions from documents you upload to a notebook. ScholarThread's chat does the same over your whole library, with your highlights and notes alongside.
- LiquidText and MarginNote are reading apps for iPad. See reading research papers on iPad.
Switching without losing anything
Whatever you choose, keep an export. Every tool on this list can export BibTeX or RIS, and those two formats move a library between almost any pair of tools. The reference formats guide explains which to use. In ScholarThread your notes are plain Markdown, so they leave with you too.
If something in this comparison is out of date or unfair to another tool, tell us and we will correct it.