Zotero on iPad in 2026: Rectoly, PaperShip, the Zotero App and GoodNotes Compared
Four ways to read and annotate Zotero papers on an iPad, compared on what comes back to Zotero, Apple Pencil, price and whether the app is still maintained. Written by Rectoly's developer, with every fact checked against the App Store and the Zotero forums.
There are four realistic ways to read and mark up a Zotero paper on an iPad: Zotero's own app, PaperShip, a note-taking app such as GoodNotes with the PDF passed to it, and Rectoly for Zotero.
I make Rectoly, so read that column with the same scepticism you would apply to any vendor's comparison. Everything below was checked on September 24, 2026 against the App Store listings and the Zotero forums, and each claim that comes from somewhere else links to it. If something is wrong, tell me and I will correct it.
The Short Version
| Zotero app | PaperShip | GoodNotes (PDF passed to it) | Rectoly for Zotero | |
|---|---|---|---|---|
| Made by | Zotero | Shazino | Goodnotes | Independent developer |
| Last App Store update | June 25, 2026 (2.0.7) | November 13, 2019 (3.8.5) | September 21, 2026 (7.1.24) | September 17, 2026 (3.0.1) |
| Price | Free | Free, annotation tools by in-app purchase | $28.99 once or $11.99 a year | $19.99 once after a 14-day trial |
| Opens your Zotero library | Yes | Sign-in reported broken since late 2025 | No, one PDF at a time via the share sheet | Yes |
| Highlights and notes go back to Zotero | Yes, as Zotero annotations | Into the PDF file | No, they stay in GoodNotes | Yes, as Zotero annotations |
| Apple Pencil ink goes back to Zotero | Yes, as Zotero ink annotations | Into the PDF file | No, it stays in GoodNotes | Yes, as Zotero ink annotations |
| Reflows two-column papers | No | No | No | Yes (Reading Mode) |
| ZotFile / ZotMoov linked files | No | No | Only by sharing the file yourself | Yes, from the synced folder on the iPad |
| Group libraries | Yes | Yes | No | Yes |
| Also on Mac and Windows | Zotero desktop | Mac (same 2019 build) | Mac | Mac and Windows, same purchase |
The rest of this article is the reasoning behind each cell.
What "Back to Zotero" Means
This is the column that matters most, and the one that is easiest to get wrong, so it comes first.
Zotero does not keep your highlights inside the PDF. It stores them as annotation items in your library, each attached to the paper, and syncs them like any other item. That is why a highlight made on the desktop appears on the phone, and why Zotero's format has a slot for freehand ink that most reference managers lack (the details are in What Zotero Does With Your Annotations on iPad).
So for each option the question is not "can I draw on the page" but "does the drawing become a Zotero annotation". If it does, it follows the paper everywhere. If it is written into the PDF file instead, Zotero's reader shows it as part of the page image and it cannot be edited, searched or deleted as an annotation. Zotero 7 can import annotations from a PDF after the fact, but a forum thread from August 2025 records that freehand ink and free-text notes do not come through.
Zotero's Own App
The reference point. It is free, made by the people who make Zotero, and its annotations are the real thing: highlights, notes, area selections and Apple Pencil ink all sync as Zotero annotations, including in group libraries. It also reads EPUBs and web snapshots, which nothing else here does.
Two things it does not do, both confirmed by Zotero staff on the forums. It does not open PDFs in an external app, and it does not read linked files, which are the PDFs that ZotFile or ZotMoov moved into a Dropbox or Google Drive folder (External pdf reader support on iPad, July 2025). If your library is built on linked files, the workaround on the forums is to move a few papers into Zotero Storage before a trip and back afterwards (iPad for reading annotating pdf books then sync back).
It also shows the PDF as laid out, so a two-column paper on an 11-inch screen means zooming and panning. Whether that bothers you depends on how much you read on the iPad and how much on a laptop.
PaperShip
PaperShip was, for years, the answer to this question. It reads a Zotero or Mendeley library and annotates PDFs with highlights, notes, drawings and stamps, and it has 926 ratings on the US App Store to show for it.
The facts as of September 2026: the current version is 3.8.5, released on November 13, 2019, and there has been no update since. Recent App Store reviews report that signing in to Zotero no longer completes (one from October 2025 describes the OAuth handshake failing, one from March 2026 says the app has not incorporated the captcha step Zotero added to its login), and a January 2025 review says annotations no longer sync to Mendeley. I have not been able to verify the current sign-in behaviour myself, so treat "broken" as "reported broken, unfixed for a year".
If it does sign in for you, remember that its annotations are written into the PDF file. Zotero's reader will show them, but as part of the page, not as annotations you can edit or extract.
GoodNotes, With the PDF Passed to It
Strictly this is not a Zotero app at all, but it is how a lot of people actually work, so it belongs here. You open the paper in Zotero's app, share the PDF to GoodNotes, and read and write there. GoodNotes' pen is excellent and its ratings (455,000 of them) reflect that.
What you give up is the library. GoodNotes holds a copy of the file, and everything you write stays in that copy. To get a highlight back into Zotero you export the annotated PDF, attach it to the item, and run Zotero's import, which brings over highlights and notes but not your handwriting (the thread linked above). Most people do not do this, and their reading notes end up living in GoodNotes permanently, separate from the paper's record in Zotero.
The price is $28.99 once or $11.99 a year for the Essential plan. If you already pay for GoodNotes for other reasons, the marginal cost is zero, which is a real argument for it.
Rectoly for Zotero
Rectoly is a paid third-party reader. It signs in to your Zotero account through the official API, reads your library and group libraries, and writes highlights, underlines, notes and Apple Pencil ink back as Zotero annotations, so they appear in Zotero on the desktop after the next sync and behave like annotations made there.
The two things that set it apart from the official app are Reading Mode, which reflows a two-column paper into one column you can highlight and write in, and linked files: if the Dropbox or Drive folder that ZotFile or ZotMoov uses is available on the iPad, Rectoly opens the PDF from there and still sends the annotations to Zotero. Papers you add on the iPad go to Zotero Storage as usual.
The honest limits. It is $19.99, once, after a 14-day trial, and Zotero's app is free. It reads PDFs only, not EPUBs or snapshots. Syncing attachment files from your own WebDAV server is supported in the Windows and Mac versions and not yet on the iPad. And it is a one-person project: the App Store listing is from September 2026, and the usage guide is where its actual behaviour is documented, including what it does not do.
Which One
- You mostly read on a laptop and occasionally check something on the iPad: Zotero's app. It is
free and its annotations are exactly right.
- Your library is built on ZotFile or ZotMoov linked files: Zotero's app cannot open them. Either
the promote-and-demote routine from the forums, or Rectoly.
- You read for hours on the iPad and two-column layout wears you down: Rectoly's Reading Mode is
the only reflow in this list.
- Handwriting is your main way of thinking and you do not need it in Zotero: GoodNotes, with the
PDF passed to it.
- PaperShip made sense until 2019. Until it is updated, it is hard to recommend to anyone who
needs to sign in today.
If you want to check the Zotero column yourself, the app is free; if you want to check the Rectoly column, the trial is 14 days and needs no card. The forum threads linked above are the best place to see what other people ran into.