Seeking help storing MarginNote files

I’m seeking assistance from anyone from @marginnote and anyone else in the community about archiving MarginNote files.

Like many other users, I’m struggling to understand how I can best archive the files that I’ve annotated with MarginNote.

The problem is that the file size of my MarginNote exports (in my case, PDFs) are so large that they become unmanageable for me to store them.

Also, it’s unclear how I can fully export an annotated file, and if I can remove it from MargiNote’s file system, so that I can archive it and free up space in MarginNote – BUT also still be able to click on the MarginNote-created URL links after the file has been archived.

By the way, I use DEVONthink to store my files, including through its offline Index interface, in case that’s helpful.

Is there a process that @marginnote and other forum users could recommend for exporting and archiving my files?

My questions are:

  1. Is there a way to reduce the file size of MarginNote-exported files (especially PDFs) so that they’re manageable to archiving?

  2. Is there a way that I can still use MarginNote-created URL links offline, after I’ve archived MarginNote-exported files?

  3. Is there some file-management set up in MarginNote that would make this process of organizing and then exporting files easier for these purposes? For instance, I’ve seen that there’s now a way for MarginNote to connect to an external folder. That doesn’t address the MarginNote-exported file size problem, but might at least help with the file management system – provided in can interface with DEVONthink. What would people here suggest?

I would appreciate any help that @marginnote and fellow users could provide.

Thank you.


Seems like you’ve posted a version of this same query elsewhere before, no?

Not criticizing, just trying to understand how this query is different than the other one — and what else has changed.

We’re all trying to find a workaround solution to MarginNote‘s bloated PDF export size, and unworkable file management. I’ve even tried addressing it on the Discord forum, but it feels like my concerns keep falling on deaf ears. So, I’m not sure what else to tell you.

But maybe someone else from MarginNote or the larger community can answer your questions and provide useful guidance. I’d be curious to hear what anyone else has to say.

Good luck, @JournoProf !


Thank you for your reply, @jprint .

Yes, you’re right: I’ve been seeking various other approaches that will enable me to work around @marginnote3’s deficits – even hack solutions that get me part of the way there.

Beyond that, however, I’d still appreciate input from @marginnote3 / @marginnote / @Support-Team in answering the questions in my original post. It feels like many of us have been addressing the same issues, especially regarding file size (particularly for PDFs) and the problems with its folder / file management. I am puzzled by why @marginnote3 / @marginnote @Support-Team hasn’t yet resolved these issues.

But again, putting that aside for the moment, I feel that @marginnote3 / @marginnote / @Support-Team could (and should) give us users guidance on how they would advise use on the life cycle of files that enter and exit MarginNote – that is, what some users have referred to as the “cradle-to-grave” of MarginNote annotated files, and how to get there.

How else do you think we can get @marginnote3 / @marginnote / @Support-Team to answer these questions and assist us?

Thank you very much again.


I hear you, and agree with all of this. I, too, have been seeking clarity about the same questions.

Honestly, I have no idea. It doesn’t seem like they’re responding to many forum posts these days. I have no idea what’s going on, and why they haven’t been responsive.

I actually relayed many of the same problems and concerns that you’ve described to @Leah_Support-Team via Discord for the iOS beta version of MarginNote (which I use far less the the MacOS version), but don’t feel like I was able to advance them effectively. So, I guess I’m at a bit of a loss as well.

I’m sorry. I share your frustration, and am likewise searching for solutions so that this app can work better for all of us.


Gotta say, it really blows my mind how NO ONE from @admin has replied to ANY of this — at all!

This is like the most basic help they could provide, and they’re totally unresponsive. It’s really quite something.

I know we constantly gripe about how little MarginNote staff actual care about users, but I’m still shocked.

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We can make a zoom when u are convenient because it takes time to make a video for every answer you can ask

Or MarginNote tech support could just answer questions on the forum.

Otherwise, what’s the point of having a forum?

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I can recommend PDF Squeezer as a very effective way of reducing PDF file size (>50%) with negligible impact on quality. It’s also simple and quick to process a large amount of PDF files in batch. It’s available via SetApp.


That’s very helpful, and I’m sure other users will appreciate that tip. Maybe even @marginnote3 can incorporate some of PDF Squeezer’s features to reduce the file size of its exports.

Beyond that, we still haven’t answered @JournoProf’s central question of storing MarginNote files – both within the app, and for archiving them after annotating them.


Hi, jprint. Recently, MNExplore have reduced the file size of MarginNote-exported files. Maybe you can have a try.
Besides,The button to export PDFs is moved into toolbar of the document tab, as the picture shows.

Exactly. I don’t get why this is so hard to spell out to users.


I’m trying best to help move this process forward with concrete suggestions.

Obviously, MarginNote syncs files through iCloud (somewhat problematically).

I’ve been talking to developers at DEVONthink Pro, and they’re hopeful there might be a way to interface MarginNote’s iCloud folder management system with their own. Obviously, that would seem to solve a lot of problems, esp. for import / export of files and interfacing with file management software (e.g., DEVONthink Pro) which many users seem to rely on.

But here’s one big problem… At present, it appress that MarginNote’s iCloud folder management system handles files stored for Documents – not for Study – and, like most users, I only annotate files in the Study mode.

To be honest, I and don’t understand the utility of Documents; I only use Study, and I expect most MarginNote users would much prefer a file management system that relies of Study.

Also, many MarginNote users have said many times before, MN’s file management system desperately needs to be overhauled so that it’s easier to store, triage and sort files – based on their subject, importance, and where they are in the annotation process (i.e., if they haven’t been ready; they’re currently being annotated in MN; or if uses have finished annotating them.

Here’s a proposed structure, based on my workflow / organization:

[“ANT” refers to files that I’ve finished annotating]

{ 1. UNsorted smart folders }

  1. Urgent [smart folder]
  2. High [smart folder]
  3. Medium [smart folder]
  4. ANT [smart folder]

{ 2. Top level: projects / topical folder ; second level / children: smart folders, per project / topic }

1. Urgent [smart folder]
2. High [smart folder]
3. Medium [smart folder]
4. ANT [smart folder]

1. Urgent [smart folder]
2. High [smart folder]
3. Medium [smart folder]
4. ANT [smart folder]

1. Urgent [smart folder]
2. High [smart folder]
3. Medium [smart folder]
4. ANT [smart folder]

So, to recap, I’d suggest:

(1) MarginNote’s iCloud folder management system can better interface with apps like DEVONthink Pro (which many users seem to rely on);

(2) MarginNote’s iCloud folder management system should be structured around Study files; not Documents files;

(3) MarginNote’s file management system desperately needs to be overhauled so that it’s easier to store, triage and sort files – based on their subject, importance, and where they are in the annotation process;

Hope this helps for things forward!

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You can easly arrange the study folder as you wish

for example
I m holding my documents in folders named SAME with study name. (arrange every folder name same with study name)
Under these big folders here are small folders named same with child mind map names

So when i get new file, i share with documents app of ipad first
second I find the big folder and put that file into small folder.
So when i open the MN, It is so easy for me to add file that I ve already put into small folder that represent child mind map of spesific study/

Yes, you can set this up just in MarginNote’s interface, though without the smart folders feature I referenced.

But I’m talking about having this structure mirror MarginNote’s iCloud folder management system.

I believe the current MarginNote iCloud folder management system centers around the Documents mode; not the Study mode.

@marginnote3 / @Leah_Support-Team / @Support-Team - please feel to weigh in on this. (I also posted this on the Discord forum, but haven’t heard back from any yet.)


Please make this happen!

I don’t know if @marginnote3 / @Leah_Support-Team / @Support-Team understand this, but THIS HAS BEEN THE MOST URGENT ISSUE for many MarginNote users!

Frankly, it’s hard to overstate this.

So, @marginnote3 / @Leah_Support-Team / @Support-TeamWill you fix this problem?

If so, when can MarginNote users expect to see these changes?

Honestly, I cannot work on MarginNote any more until these file management issues are resolved. At the very least, these should be an easier way for files to be managed in iCloud’s so that they better interface with other file management apps.

Thank you.

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This. All of this…

Any joy @marginnote3 / @Leah_Support-Team / @Support-Team ??