How to sync your Zotero library with ScholarThread

Most researchers already keep their references somewhere. If that somewhere is Zotero, you do not need to rebuild your library from scratch to start reading and taking notes in ScholarThread — you connect the two, your collections appear in the Library sidebar, and you let them stay in step.

This guide walks through the whole flow: connecting your account, finding what was imported, understanding how syncing behaves, and — on the Pro plan — sending individual papers back to Zotero.

Before you start

You will need a Zotero account with some references in it. PDFs stored in Zotero's own storage come across too, so it helps to have your files attached in Zotero before you connect.

Connecting imports your collections, so there is nothing to pick up front. If your library is very large, expect the first import to take a while; it runs in the background and you can keep working while it does.

Step 1 — Connect your Zotero account

Open Settings → Connections and choose Connect Zotero on the Zotero card. You will be sent to Zotero to authorise ScholarThread. This uses Zotero's standard OAuth flow, so you are approving access on Zotero's own site — ScholarThread never sees your Zotero password.

ScholarThread asks Zotero for access to your library, including write access. Approve it and you will land back in ScholarThread with the connection established. If you decline write access on Zotero's page, importing still works; only the Pro push-back described below needs it.

Step 2 — Find your collections in the Library

As soon as you are connected, ScholarThread starts importing your Zotero collections and the papers in them. You do not tick collections to import — they are added to the collection tree in the Library sidebar, next to any collections you create in ScholarThread, with sub-collections nested under their parents.

A few things worth knowing:

• Imports run in the background, so papers start appearing in the Library while the rest are still arriving.
• Refresh a single collection with the refresh icon next to it in the sidebar. The icon spins while it syncs and shows a tick when it finishes.
• Zotero notes and attachments are not imported as papers. Each item with a title becomes a paper; PDFs attached to it are fetched where they are within the size limit.

Step 3 — Read and annotate

Open any paper in your library. If it has a PDF attached, it opens in the built-in reader, where you can highlight passages and attach margin notes. Highlights and notes are anchored to the exact location in the document, so when you come back a month later the context is still there.

This is the point of connecting Zotero rather than just exporting a bibliography: the references, the files, and your thinking about them live in one place.

Keeping the library current

Your Zotero connection card in Settings → Connections says "Connected to Zotero" and holds the controls for keeping things in step:

• Background sync. Switch on Sync automatically with Zotero and pick a Sync interval (every hour, 6, 12 or 24 hours). The card shows when it last synced. New and updated papers then appear without you doing anything.
• Manual refresh. Use the refresh icon next to a collection in the sidebar to sync just that collection right now.
• If syncing keeps failing, the card shows "Sync failing repeatedly". Your Zotero authorisation may have expired; use Disconnect, then Connect Zotero again.

Expand

Sending papers back to Zotero (Pro)

By default the flow is one-way: Zotero to ScholarThread. On the Pro plan, with write access granted to ScholarThread on Zotero, you can also push papers the other way:

• Per paper. Open a paper that is not in Zotero yet and click the Z badge in its detail view (it reads "Sync to Zotero"). The paper is created in your Zotero library in the background. Click the badge again on a synced paper to choose Remove from Zotero — this deletes it from your Zotero library and cannot be undone, but the paper stays in ScholarThread.
• When adding a paper. In the Add paper form, tick Also push to Zotero and choose a target Zotero collection (or the library root).

In the papers list, the plain Z simply marks a paper that is synced with Zotero.

Syncing a paper sends the reference itself — its metadata, collections and PDF. Notes and highlights you create in ScholarThread stay in ScholarThread; they are not written into Zotero. On the free plan, Zotero import is read-only.

Disconnecting and clearing

Two separate buttons on the Zotero card, each behind a confirmation:

• Disconnect removes the connection. Papers already imported stay in your library.
• Clear imported papers deletes the papers that were imported from Zotero from ScholarThread, together with their Zotero collections here. This cannot be undone. It affects ScholarThread's copy only. You can then re-import from the sidebar refresh icons, or disconnect to start from a clean slate.

There is no separate "reconnect" button: to reconnect, disconnect and then choose Connect Zotero again.

Troubleshooting

• Nothing imported after connecting. Give it a few minutes for a large library, then check the Library sidebar. You can re-run a collection with its refresh icon.
• PDFs are missing. The files need to be attached in Zotero in a way ScholarThread can download them. References with no attachment come across as metadata only.
• The Z badge in a paper's detail view is not clickable. Per-paper sync needs the Pro plan and write access on your Zotero connection. If you declined write access, disconnect and connect again, and approve it this time.

The short version

Connect Zotero in Settings → Connections, find your collections in the Library sidebar, and turn on background sync if you want them kept fresh. On Pro, the Z badge in a paper's detail view and Also push to Zotero on Add paper send individual papers back.