ScholarThread for Zotero users: keep Zotero, add reading, notes and AI
ScholarThread works alongside Zotero rather than replacing it. Connect once, then read and annotate your Zotero papers on the web, iPad and iPhone, take linked notes, and ask questions answered from your own library.
Short answer: you do not have to choose between Zotero and ScholarThread. Keep Zotero for collecting references and citing them while you write. Connect it to ScholarThread once, and your collections appear in a reader, a notebook and a chat that answers from your own papers, on the web and in the iPhone and iPad app.
Most researchers we talk to already have years of references in Zotero, and that library is worth keeping. ScholarThread is built for what happens after a paper is saved: reading it closely, writing notes that point back to the passage they came from, seeing how papers connect, and asking questions across everything you have read.
Which job goes where
| What you are doing | Where to do it | Why |
|---|---|---|
| Saving references from a journal page | Zotero, or the ScholarThread browser extension | Both work. Items saved in Zotero reach ScholarThread on the next sync. |
| Inserting citations while writing in Word, LibreOffice or Google Docs | Zotero | ScholarThread has no word-processor plugin. It can copy a citation, or export BibTeX, RIS or a bibliography in a CSL style. |
| Reading and highlighting a paper | ScholarThread | One reader for PDFs and EPUBs on the web, iPad and iPhone, with five highlight colours, a note on every highlight, and Apple Pencil on iPad. |
| Writing literature and concept notes | ScholarThread | Notes link to papers, passages and each other, and export as plain Markdown to Obsidian or a Git repository. |
| Asking a question across many papers | ScholarThread | Chat answers from your library and cites the passage behind each claim. |
| Seeing how papers and notes connect | ScholarThread | The knowledge graph shows what cites what, what links where, and what is still unconnected. |
How the connection works
- In ScholarThread, open Settings → Connections and choose Connect Zotero.
- Approve access on Zotero's own site. This is Zotero's standard sign-in flow, so ScholarThread never sees your Zotero password.
- Your collections import in the background and appear in the Library sidebar, with sub-collections under their parents. PDFs kept in Zotero's own storage come across too, within the size limit.
After that, the refresh icon next to a collection syncs just that collection, and Sync automatically with Zotero keeps the whole library fresh on an interval you choose. Zotero notes and standalone attachments are not imported as papers; every item with a title is.
On the Free plan the connection is read-only: ScholarThread never changes your Zotero library. On Pro you can also push individual papers back to Zotero (the reference, its collections and its PDF). Your ScholarThread notes and highlights stay in ScholarThread; they are not written into Zotero. The Zotero sync guide has every step.
What it costs
The Zotero connection is included on the Free plan, along with sync across devices and 100 MB of cloud storage for PDFs. Pro adds 10 GB of storage, pushing papers back to Zotero, a monthly allowance of AI credits for chat and assisted notes, and the MCP server for your own AI assistant. There is an academic price for eligible accounts. Current prices are on the pricing page.
Privacy, briefly
- Your library, notes and PDFs are stored in AWS's Stockholm region (eu-north-1).
- AI features run on Amazon Bedrock in AWS's EU regions. A few optional chat models may run outside the EU; they stay locked until you consent, and you can withdraw consent at any time.
- Your content is not used to train AI models.
- Your Zotero access key is stored encrypted.
The privacy policy has the full detail.
What ScholarThread does not do (yet)
- No citation plugin for Word, LibreOffice or Google Docs. Keep using Zotero's for that.
- Notes and highlights do not go back into Zotero. Pushing a paper to Zotero sends the reference and its PDF, not your annotations.
- Handwriting is iPad and iPhone only. The web reader shows your ink but cannot add to it.
- Android is in development. Today it is the web plus the iPhone and iPad app.
- It is new. ScholarThread launched in 2026; Zotero has been around since 2006.
Questions Zotero users ask
Do I have to stop using Zotero?
No. Most people keep Zotero as their reference library and citation tool and use ScholarThread for reading, notes and questions.
Will connecting change anything in my Zotero library?
Not unless you choose to. Importing only reads from Zotero. The only thing that writes to Zotero is pushing a paper back, which is a Pro feature you start yourself, one paper at a time.
Can I use ScholarThread without Zotero?
Yes. You can add papers by uploading a PDF, by DOI, by pasting a BibTeX entry, from OpenAlex search, or with the browser extension. See adding a paper.
I write in LaTeX. Does it fit?
Export a collection, a search result or the whole library as BibTeX, or paste BibTeX entries in to add papers. The reference formats guide explains which format to use when.
Try it
Connect Zotero, open a paper you are reading this week, and follow the literature-review note-taking workflow. If something here is out of date or wrong, tell us.