What Zotero Does With Your Annotations on iPad

You draw a line under a sentence on the iPad. Where does it live now, and will it still be there when you open the same paper on your laptop?

For Zotero the answer is better than it is almost anywhere else, and it comes down to one detail of the format.

What Zotero Stores as an Annotation

Zotero's PDF reader gives you highlighting, underlining, notes, area selection, and a drawing tool. All of them are stored in your library as annotations and sync with everything else.

The interesting one is the last. A Zotero ink annotation does not record a rectangle around where you drew — it records the strokes themselves: the paths your pen took, and the width they were drawn at, on a given page.

That sounds like an implementation detail. It is the difference between your handwriting being part of your library and your handwriting being a picture.

Why a Slot for Ink Matters

Most reference managers model an annotation as a type plus a rectangle on a page. That works for things you do to text — mark a span, pin a note to a spot. It has no way to describe a line that curves.

Mendeley is the clearest example: its annotation model covers highlights, sticky notes and underlines, each positioned by a bounding rectangle, and there is no ink type at all. Handwriting in a Mendeley library has to be kept outside the annotation model or flattened into the file. (That case is worked through in How to Annotate Mendeley PDFs on iPad.)

Zotero made a different call. Because ink is a first-class annotation, handwriting done on an iPad can be the same object as everything else you marked: it syncs, it belongs to the item, it can be deleted or edited later, and it is there on the desktop.

For anyone who reads with a stylus, this is the single most consequential difference between the two libraries.

If You Annotate in Zotero's Own Reader

Marks made in Zotero's reader are Zotero annotations by definition. They sync, they show up on your other devices, nothing is stranded. This is the baseline everything else is measured against.

If You Annotate in a Separate PDF App

Download the attachment, open it somewhere else, mark it up there.

Those marks belong to that copy of the file, in that app. Zotero does not know they happened, and the item in your library still points at the version without them. Some readers can export a flattened copy with the marks burned in, which you can attach back — but a flattened annotation is an image of a mark rather than a mark. It cannot be searched, filtered by colour, or edited.

This is the route where a semester of reading quietly ends up in the wrong place.

If You Annotate in an App That Syncs

An app signed in to your Zotero account can create annotations through the same API the desktop uses. A highlight made on the iPad becomes a highlight in your library. A stroke made with Apple Pencil becomes an ink annotation, with its paths, on that page.

That is the whole promise of the format being open enough to describe a pen stroke: the app on the iPad and the app on your desk are writing the same kind of object.

The One Place Ink Cannot Be a Zotero Annotation

There is an exception, and it is worth understanding because it is not an app limitation.

A Zotero ink annotation is anchored to page coordinates — a stroke at this position on page 7. That requires a page. When a two-column paper is reflowed into a single readable column, the text is no longer laid out on the original page: it has been re-flowed to fit your screen, at whatever size you chose. A stroke drawn on that surface has no page coordinates to record, because it was not drawn on a page.

So handwriting made while reading reflowed text cannot be a Zotero ink annotation. It has to be kept some other way. Handwriting drawn directly on the PDF page has no such problem and syncs normally.

Where Rectoly Fits

Rectoly for Zotero signs in to your Zotero account and writes real annotations. Highlights, underlines and notes go to your library, and Apple Pencil strokes on the PDF page become Zotero ink annotations — the same objects Zotero's own reader creates, visible on the desktop.

Handwriting made in Reading Mode is the exception above. Since there is no page position to store, it travels between your own Apple devices through iCloud rather than through Zotero, and can be exported as JSON. It is kept, and it is not tied to one device; it just is not something the Zotero format can hold.

Marks made offline are stored on the device and go up when you reconnect. If a sync would erase most of a paper's handwriting, or two devices disagree, Rectoly stops and tells you rather than resolving it quietly.

Frequently Asked Questions

Does Apple Pencil handwriting sync to Zotero?

Handwriting drawn on the PDF page does, as an ink annotation, so it appears on the desktop like any other annotation. Handwriting drawn on reflowed text does not, because there is no page position to record it against.

Will annotations I made on the desktop show up on the iPad?

Yes, with an app that reads as well as writes. Annotations are library data, not app data.

If I mark up a PDF in another reader, can I get those marks into Zotero?

Not as annotations. You can attach a flattened copy, but the result is a picture of your marks rather than marks Zotero can search or edit.

Is this different in Mendeley?

Yes, and it is the main difference for anyone who writes by hand. Mendeley's annotation model has no ink type, so handwriting cannot become a Mendeley annotation at all. The details are in How to Annotate Mendeley PDFs on iPad.

Conclusion

Reference managers are usually compared on citation styles and storage quotas. If you read with a stylus, the more useful question is whether the format has a shape for what you draw.

Zotero's does. That is worth knowing before you decide where a few years of margin notes are going to live.