How to sync your Zotero library with ScholarThread (and enable write-back)

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, pick the collections you care about, and let them stay in step.

This guide walks through the whole flow: connecting your account, choosing what to import, understanding how syncing behaves, and — the part people most often get stuck on — granting the permission that lets ScholarThread write notes back into Zotero.

Before you start

You will need a Zotero account and at least one collection with references in it. Web attachments and PDFs stored in Zotero's own storage (or a linked WebDAV) come across too, so it helps to have your files attached in Zotero before you import.

If your library is very large, decide up front whether you want everything or just a working subset. You can always add more collections later, and starting with the two or three collections tied to your current project keeps the first sync fast and the interface uncluttered.

Step 1 — Connect your Zotero account

Open Settings → Connections and choose Connect Zotero. 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.

When Zotero asks what to grant, there are two decisions that matter:

• Read access to your library. This is required — without it there is nothing to import.
• Write access (also called "Allow write access"). This is optional, and it is what lets notes and highlights you create in ScholarThread flow back into Zotero. More on this below.

Approve the access and you will land back in ScholarThread with the connection established.

Step 2 — Choose which collections to import

After connecting, you will see your Zotero collection tree. Rather than pulling in your entire library by default, ScholarThread lets you select collections deliberately. Tick the ones you want; leave the rest.

A few things worth knowing:

• Sub-collections can be included with their parent, so selecting a top-level collection brings the branch beneath it.
• The same reference in two collections is not duplicated — it is one paper that appears in both places, exactly as in Zotero.
• Imports stream page by page, so a large collection starts appearing before the whole thing has finished. You do not have to wait for a spinner to clear before you begin reading.

Step 3 — Read and annotate

Once a collection is in, open any paper. If it has a PDF or EPUB attachment, 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.

Step 4 — Enable write-back

By default the sync is one-way: Zotero → ScholarThread. If you want your ScholarThread notes to appear in Zotero as well, you need write access — and if you connected with read-only access at first, you will need to re-authorise.

Here is the reliable way to turn it on:

1. In Zotero, go to Settings → Security (on the web, this is under your account's Feed/API or Security settings).
2. Find the ScholarThread entry under authorised applications.
3. Make sure "Allow write access" is enabled, and — if you use group libraries — that notes permission is granted for the relevant library.
4. Back in ScholarThread, open Settings → Connections and choose Reconnect Zotero so the new permission is picked up.
5. Confirm the write scope when Zotero prompts you.

Once write-back is on, notes you create against a paper are pushed to that item in Zotero as child notes. If you later edit the note in ScholarThread, the change is reflected on the next sync.

A quick sanity check: create a short test note on any paper, trigger a sync, and open that item in Zotero. If the note appears as a child note, write-back is working. If it does not, the permission almost certainly did not take — re-check step 3.

How conflicts are handled

Two-way sync always raises the same question: what happens if the same thing changes in both places? ScholarThread follows a last-writer-wins rule for note content — the most recent edit is the one that survives. In practice conflicts are rare, because notes tend to be edited in one tool at a time, but it is worth knowing the rule so nothing surprises you.

If you routinely edit the same note in both Zotero and ScholarThread, treat one of them as the source of truth for that note to avoid overwriting your own work.

Keeping the library current

New references you add in Zotero show up in ScholarThread on the next sync. You can trigger a sync manually, and background auto-sync keeps the two aligned without you having to think about it. If a paper disappears from a Zotero collection, it stops appearing in that collection in ScholarThread too — the structure mirrors your library rather than drifting from it.

Troubleshooting

• Nothing imported after connecting. Check that you actually selected at least one collection — connecting alone does not import anything.
• PDFs are missing. The files need to be attached in Zotero (either Zotero storage or a linked file that Zotero can serve). References with no attachment come across as metadata only.
• Notes are not appearing in Zotero. This is almost always the write-access permission. Re-check it in Zotero's security settings and reconnect.
• A group library is not showing. Group libraries have their own permissions; make sure your Zotero account has access and that you granted the relevant scope.

The short version

Connect Zotero, choose your collections, and read. If you want notes to travel back to Zotero, grant write access and reconnect. From there your references, your files, and your notes stay in one library that reflects how you actually work — which is the whole idea.