How to Make Your Zotero PDF Annotations Available for Mobile

One feature with some substantial upgrades in Zotero 7 is the built-in PDF viewer and annotator.¹ For a long time, I’ve not used this feature. But seeing the updates that it’s gotten, I decided to give it a try, and I really do like what the developers have done with it.

One potentially complicating factor, though, is how Zotero stores annotations in its database, not in the PDF. Zotero also doesn’t directly integrate with cloud storage providers.

This situation means that you can’t synchronize a PDF with, say, OneDrive and then open it with all its annotations on Zotero’s mobile apps. It also means that, if you open your PDF with a generic PDF reader, you won’t see the annotations that you’ve saved for that PDF in your Zotero database.

This said, in Zotero 7, you can export these annotations to a generic-PDF-reader-accessible format any time you like from File > Save As …. So, the annotations aren’t captive in Zotero, which is very nice.

All of this means that, if you want to use Zotero’s PDF viewer and annotator on the desktop and also want to access those annotations on a mobile app, you have 4 options for how you do so.

If you need to exchange files between the desktop client and a mobile app frequently, option 1 or 2 will give you a significantly smoother experience. If you do so only infrequently, option 3 or 4 are also workable.

1. Use Zotero storage.

By far the simplest method is to use Zotero’s own storage. You get 300 MB free with your account. When you run out of space, you can upgrade your storage plan appropriately.

Using this option, everything just works. You annotate a PDF on the desktop, synchronize your changes, open the PDF on mobile, pick up where you left off, and vice versa.

2. Use WebDAV storage.

Zotero doesn’t directly integrate with cloud storage providers. But Zotero does support synchronizing your PDFs via the WebDAV protocol.

At present, this feature is only available in the desktop clients and iOS app. But the feature is slated to make it into the Android app before that app emerges from beta.²

If you already have WebDAV configured successfully for Zotero on your desktop, you just need to log into the same WebDAV account in the Zotero mobile app. From there, your experience should be nearly identical to what it would be if you were to use Zotero storage.

3. Use a group library.

When logged into your Zotero account in a browser, you can create a private group library (e.g., named “Mobile Reading”). Just like your default “My Library,” a private group library will be accessible only to you unless you invite other users to access it as well.

3.1. Configure a private group library.

Once created online, you’ll see your new library in the “Group Libraries” section of Zotero the next time the desktop client synchronizes. You can then choose to synchronize this group library’s attachments to Zotero storage (Edit > Settings > Sync), even if you don’t synchronize your regular library’s attachments there.

Configured this way, Zotero will synchronize any PDFs that you include in your private group library with your Zotero account storage, including the 300 MB that your account provides for free. If you only ever need to “check out” a modest number of items for mobile reading, this 300 MB might be totally sufficient.

3.2. Copy an item to your private group library for mobile reading.

Any time you want to read something from your regular library on mobile, just drag the item to copy it to your private group library. After Zotero synchronizes, you’ll be ready to read on mobile.

At the same time, you’ll still see the same item in your regular Zotero library. Do not delete this original item. You need this item both now and later.

A challenge with this approach is that Zotero doesn’t allow you to move an item from one library to another. You can only copy the item. Zotero has this limitation because links to Zotero items from documents where you’ve cited those items are library-specific.

If you delete from one library an item that you’ve cited (as happens in a move operation), you’ll break the citation links to that item. The next time Zotero updates a citation to that now-gone item, you’ll get an error message that gives you options about how to mitigate the damage.

So, when you copy an item to a different library, don’t delete the original—especially if you’ve cited it in a document but really even if you don’t think you have. You don’t want to forget about a place where you’ve cited that item before and then create work for yourself that you could have avoided.

3.3. Annotate your PDF and synchronize your annotations.

Instead, when you’re done working with the attachment on the Zotero mobile client, synchronize your changes there and on the desktop. At this point, you’ll have

• one item (with the updated attachment annotations) in your private group library and
• one item (with the outdated attachment annotations) in your regular library.

3.4. Merge your private group library item into your main library.

To merge these items back together,

1. Copy the item from your private group library into your regular library. Now, you’ll have two copies of this item in your regular library and one in the private group library.
2. Delete the item in your private group library. Doing so will leave you with two copies of this item in your regular library, one with the outdated attachment annotations and one with the updated annotations.
3. Select both items in your regular library, right-click, and choose to Merge Items…. Or you can find the pair in your regular library’s Duplicate Items section, and click the button to Merge 2 items. This step will condense the two items, each with its own attachment, into one item with two attachments.
4. Open both attachments, and identify which one has the updated annotations.
5. Delete the attachment with the outdated annotations.

Having Zotero merge the items allows the database to retain both the PDF annotations you’ve added and connections to any citations you’ve made of either item.

4. Export and import annotations.

If you want to use the Zotero mobile client to annotate your PDF, then this option isn’t for you. On the other hand, if you’re comfortable using another app (e.g., Acrobat Reader) to annotate the PDF on mobile, then you can consider this approach.

That said, for this approach, you should also be running the latest release of Zotero 7. Zotero 6 doesn’t do nearly as well at the import step below, and you may end up losing annotations at that point in the process.

4.1. Export your annotations.

To begin,

1. Find the PDF you want to read on your mobile device.
2. Open that file in Zotero so that you can see its annotations.
3. Do File > Save As…, and save the file to a place where you can make it available to your mobile device. This could be a cloud storage folder that you have configured both on your desktop and your mobile device.

4.2. Work with your PDF on a generic mobile reader.

Once you have your PDF on your mobile device, annotate it as you wish in the app of your choice. You should have several options. But it may be prudent to do a test run to ensure that your mobile PDF reader will save your annotations in a way that Zotero can read and import them.

4.3. Reimport your PDF.

When you’re ready to bring your PDF and its annotations back into Zotero’s desktop application,

1. Add the file to its corresponding library item as a new attachment. You’ll then have the old attachment that didn’t get synchronized to your mobile device and the new one that you’re importing.
2. Delete the old attachment. This step will leave you with just the one attachment that you’re re-importing. You can always restore your old attachment from your Zotero trash can if need be.
3. Open the remaining (new) attachment. Wait for a few moments while the annotations load.
4. Do File > Import Annotations…. This step will turn the locked PDF annotations back into annotations saved in and manipulable by Zotero. Some of these annotations may be annotations that you previously exported from Zotero. Others may be ones that you initially created on your mobile PDF reader. Zotero seems to do a good job ingesting all of these.

This said, again, you may want to do some testing before relying too heavily on this procedure. You want to be sure the particular mobile PDF reader you choose won’t create annotations that annotations

• don’t save to the PDF itself,
• aren’t readable by Zotero, or
• aren’t something Zotero can import.

Conclusion

From its inception, Zotero’s PDF annotation experience has grown by leaps and bounds. If you work strictly with the Zotero desktop clients, the experience is seamless. Using a Zotero storage plan extends this seamless experience to Zotero’s mobile apps as well. But even if you don’t use a Zotero storage plan, you still have several, workable options for how to ferry PDFs and their annotations between the desktop client and mobile apps.

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1. Header image provided by Zotero via Twitter. ↩

2. See Dan Stillman, “Available for Beta Testing: Zotero for Android,” Zotero Forums, 25 December 2023 and especially the following comment by Sebastian Karcher, a.k.a. adamsmith, on 13 January 2024. ↩