Best Option for Managing PDF's

Sorry, had my numbering wrong. I referred to Zotero 6 as Zotero 7 and Zotero 5 as 6. Updated!

DEVONthink and Zotero are both great options if you want to be able to quickly change the status of an item with the application or removal of a tag (perhaps Bookends as well, but not sure; I purchased it couple of years ago but only a few days ago started to use—definitely takes some getting used to). @ryanjamurphy has plenty of experience with both DEVONthink and Bookends, so perhaps he could chime in if he sees fit to do so.

One hundred PDFs ain’t a huge number, though, so plenty of the apps for editing PDFs that others have mentioned should work just fine as well.

For whatever it’s worth, I created a somewhat in-depth evaluation of PDF-annotation apps last December for a former student of mine who’s now finishing up law school (and for myself because I was trying to figure out which app would work best for my own purposes).

You can check out the full piece on the page from my Notion account that’s here. One thing you’ll see there is that although I love Highlights, I really wish it gave you the option of handwriting notes on your PDFs.

In the coming weeks, I plan on updating the piece and releasing it in a series of posts (and emails to subscribers) via my Ghost website: <–If you subscribe, I will feel less lonely :joy:

Apps compared: GoodNotes, GoodReader, Highlights, iAnnotate, PDF Expert, Zotero iOS

Also discussed: LiquidText, MarginNote, Nebo, Notability, Obsidian, ZoomNotes, Zotero for Mac

Also mentioned: Collanote, Flexcil, Roam, Scribble (iPad feature), TextSoap (for removing unwanted characters and spaces in text), Zettlr, ZKN3, Zotfile (Zotero add-on)


I, at one time, used Paperless by Mariner Software. I can’t tell if it has been updated lately, and it created its own database which was a pain. I moved onto Yep, and found that to be very good as far as organizing and renaming PDF files where they were located, instead of creating another database. I have since just thrown all of my PDF’s into EagleFiler, which I love the best because the PDFs are there amongst all of my other files…

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So glad I found this. I was recently setting out to do such thing myself (and maybe blog about it).

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I’m liking Highlights as my PDF editor of choice. Works well on both Mac and iPad


Cailbre is awsome. It can dedrm so you can PDF books and allows you to create PDFs of different sizes reflowing the text. You can change font, font size, etc. I often turn a chapter into an A4 PDF so I can better mark it up with generous margins or print to read and mark up.


I use calibre to get all my kindle books converted to EPUB and into the Reader app from Readwise for highlighting.

It’s also my BU of kindle books in DeDRMed formats