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PDF++ Walkthrough for Highlighting on iPad

TL;DR

I was using Zotero and Obsidian together, then found PDF++ and started experimenting until I got a low friction highlighting workflow working directly in Obsidian on iPad.

What it does

Lets me highlight PDFs directly in Obsidian on iPad
Appends highlights into a note that is already open
Places the page link right after the selected text
Keeps Zotero mostly for citation eas

Watch the walkthrough

Watch on YouTube →

The details

Hello friends,

I am falling more and more in love with Obsidian over the years and want to share some new workflow ideas with you.

I studied with Tiago Forte from BASB for about 4 years from 2019 onwards and he had such an emphasis on capturing information. For me I love Obsidian as I’m starting to use it with on-device LLMs too.

Currently I am coming to the end of my Masters and I was using Zotero and Obsidian together. Then I found out about PDF++ and only kept using Zotero for the citation ease and the PDF highlighting experience on iPad.

I’ve been experimenting with the settings on iPad to get a low friction system working for highlighting PDFs directly in Obsidian with PDF++.

Setting up the copy text format in PDF++

These are my settings and I think they work well.

Custom copy format

"Text" - "{{selection}}" {{linkWithDisplay}}

This places the link to the text as the page number following the selected text.

"Mainstream psychiatry follows this tradition. Over the past decade the Departments of Defense and Veterans Affairs combined have spent over $4.5 billion on antidepressants, antipsychotics, and antianxiety drugs." p.186

For publishing on the site, a footnote reads more cleanly than the raw Obsidian PDF link.

As markdown it can look like this:

"Mainstream psychiatry follows this tradition. Over the past decade the Departments of Defense and Veterans Affairs combined have spent over $4.5 billion on antidepressants, antipsychotics, and antianxiety drugs."[^1]

[^1]: Van der Kolk, B. (2015). *The body keeps the score: Mind, brain and body in the transformation of trauma* (p. 186).

Setting up a note to append highlights to

Create a new note with all the properties, titles and etc that works for your system. I use an elaborate system that pulls in all the properties from Zotero and pre-fills them into Obsidian.

Settings in PDF++ for selecting highlights on iPad

Enable Auto Copy.
Enable Auto Paste.
Under Auto Paste change the setting for Target Markdown File to Paste Links to to Last active & open md if any, otherwise last pasted.
Disable Focus Editor After Auto-Pasting.
Disable Respect Current Cursor Position.
Enable Blank line above the appended content.
Under General, disable Open target markdown file if not opened.

This last option is the main one to select so that when you highlight text it does not keep opening up the note and pulling you away from the PDF.

Setup to start highlighting

Open the note for the highlights to be copied into as a new tab.
Make sure Auto Highlight and Auto Paste are enabled. They are in the ribbon as a text marker and clipboard with an outgoing arrow icon.
Highlight your first row of text.
Click over to the tab note and check if it has pasted.
Have fun, get smart, share ideas and be kindly cheeky.

I hope this helps folks. I made a video on it too. For now this is still the easiest way I know.

Why I like this setup

For me the real value is that it feels low friction enough to actually use. Zotero is still great, especially for citations, but this gets me much closer to reading and capturing in one place.

I like that the highlights land in Markdown, stay linked to the source, and can fit into a broader Obsidian system without too much ceremony.

If you already have a Zotero workflow, this does not have to replace it. It just gives you another option if the iPad highlighting experience inside Obsidian is what you have been missing.

Little nerdy solution for the six people who need it.