PDF Annotation Workflow for Students?

I’m wondering if there’s a workflow or method to directly annotate PDFs in Obsidian. Maybe I’m trying to shove a task Obsidian’s not meant to do.

The whole semester I’ve been trying to fully use Obsidian for my Biomedicine course, but I feel like it isn’t sticking; there’s way too much information to input and too little time to process it, make smaller, more atomic notes, and then maybe make flashcards for those notes.

I’ve been using a mix of Obsidian and Onenote. I input the provided lecture slides into Onenote and directly annotate my ideas into it. In this method, the information is ‘complete’: There’s the information that’s already provided in the lecture slides and then whatever a lecturer rambles is also on it. This saves a considerable amount of time because the structure of my notes are more top-down (conventional) and I don’t have to write as much stuff, which means I can make more practice questions + There’s more visual cues to improve info retention and retrieval.

The problem with this method is that it’s hard to get to a certain information. Onenote’s OCR is pretty good, but it’s still hard to find information when it’s all over the place and there’s a lot of it.

On the other hand, Obsidian seem to not be able to search text in PDFs easily, does not have automatic OCR of any kind (There seems to be 2 methods for this already though [1, 2], albeit they’re both manual - in the sense that you have to pick a picture and then it does the OCR for you).

I’ve been thinking of just inputting PDFs as individual images and then extracting the text from it as comments below the images, so that it makes them searchable, and then just writing out my thoughts and further ideas below the comments. This feels like such a roundabout way to do something, hence my initial comments that I’m probably shoving Obsidian to do something it’s not made to do (for now).

Or maybe I’m missing something? Thoughts?


i think obsidian can potentially do this kind of stuff. It think it is a good idea to annotate pdf inside obsidian. I am trying to do it with epub by converting it first to markdown and it looks like a fine workflow till now. Altho i am not sure yet.

for pdfs we can convert pdf docs to markdown too by a plugin insdie obsidian for Ctrl + F ing. also better pdf view plugin can help for showing a single page of a pdf doc, making it possible to comment below it. so some tools are already available for such a workflow.

For reference, see also these somewhat related threads:


As @msteffens mentioned, there are tools that are built for PDF annotation. I use MarginNote extensively. A MarginNote note has a URI that I can use in Obsidian - clicking on it in Obsidian will make the note come up in MarginNote. Conversely, I put Obsidian URIs in my MarginNote 3 notes, so I can refer to more general notes that I take. This works quite well.

I think it would be difficult for Obsidian to have all the features of MarginNote or LiquidText. Of course, the downside is that these PDF annotation tools are expensive. Also, while MarginNote is an amazing program, it is not the easiest to use.

an idea if you are open to jumping to other tools for the PDF side of things:

  • Zotero for reference management
  • Any PDF reader for annotations. I use PDF XChange Editor (Free)
  • Zotfile plugin to extract PDF annotations.
  • MDNotes plugin
    • translates the extracted annotations into markdown
    • exports MD file to my Obsidian “Inbox” folder

It’s a pretty short jump from reading/taking notes to the finished, atomic notes in Obsidian, each of which links to the page in the original PDF I’m referring to. I.e. I end up with the notes I made while reading, plus a link in each note that opens the PDF to the place where I originally made the note.

That’s the basic setup. Start with that if that much sounds good.


You can optionally keep literature notes (sounds like you are familiar with Ahrens’ Zettelkasten method) in Obsidian. It’s not necessary - by Ahrens’ method you really only need your permanent notes in Obsidian. I use a plugin called Citations that very easily makes a note linking back to Zotero. I use those for a kind of bastardized literature note.

My literature notes:

  • copy extracted notes into literature note for a reading session, usually a formatted section of a book or a reading session of x minutes
  • organize, rewrite more concisely, trying to
    • resynthesize ideas
    • make the most dense presentation possible for future reading
  • use a plugin called Note Refactor to split the good, atomic parts into notes

I have no sense of how effective / time-efficient I am relative to a large sample of people reading / writing this way, but I can tell you that I’m about twice as productive as when I was doing things more manually.

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