While I currently don’t store PDF’s, or really anything but text files, in Obsidian I know that many other users like to have everything in Obsidian. I’m still also not entirely sold on Zotero for my storage needs after leaving DEVONthink behind so let’s look into how Obsidian handles PDF files.
Native PDF Handling
To start, Obsidian has come a decent way with its own native PDF handling. Copy and paste a PDF into your Obsidian note and it will be added to your Assets folder and be embedded in your note.
With the PDF embedded in Obsidian you can then start reading it, though I found the size of the embedded document to small, even on a 43″ 4k screen. But Obsidian still has you covered because under the 3 dots menu you can choose to open the PDF in a few different ways. I picked
Open to right and got an excellent split screen view of my note and the PDF.
Another good option would be to open the PDF in your default PDF viewing application since that would allow you to highlight the PDF, which is a feature that Obsidian doesn’t bring to the table. Once you’re editing the PDF in your default PDF application, any highlights can be shown back in Obsidian if you save the PDF back in the same location replacing the existing PDF document.
While DEVONthink did allow PDF highlighting directly in the application, this is not a feature I ever used. I take notes on PDFs in plaintext in Obsidian and let the PDF stay where it is unmodified.
If you really need/want to annotate PDFs directly in Obsidian then you can take a look at Obsidian Annotator, but there are a bunch of caveats on it’s use so after a bit of messing around I stopped trying it out. The biggest issue being that it doesn’t show annotations that were changed on other platforms. This means I can’t swap working between my Linux laptop, iPad and Mac Studio seamlessly and have all the same data I wanted on each platform.
So, with the good native handling of PDFs in Obsidian, I’m now wondering if I should just keep all my “inbox” of reading directly in Obsidian and not worry about some other application like Zotero or DEVONthink.
-  You can set your assets folder location in Obsidian settings. I use zz – Assets as my location for the few assets I have in Obsidian