Embedded Zotero Reader in Obsidian – How do you handle PDF reading & highlights?

[ZheXin]

Hey all

A lot of you have insanely polished Obsidian + reading setups. Mine… isn’t (yet). I’m building a plugin to reduce the friction and would love to learn from your battle-tested habits before I lock in the storage layer.

I’ve embedded the Zotero reader (PDF / EPUB / HTML snapshot) directly inside Obsidian—no Zotero DB/API calls. Everything (reader + highlights) lives in the vault and syncs like normal. Basic highlighting & annotations already work:

What I need from you: How are you currently managing PDF highlights + Markdown notes? What’s working / painful?

Models I’m Considering

1. Single markdown file per source – every highlight as a block.

2. Hybrid “promote on interaction” – raw highlights (geometry + exact text) stay in a JSON file; a Markdown block (with block ref) is created only when you comment / tag / edit it.

3. One markdown file per annotation – maximal granularity, lots of tiny files.

4. All in JSON – plugin UI renders everything; minimal native Markdown surface.

Quick Questions (reply to any subset)

• Your current setup (plugins, exports, scripts, manual glue)?

• Biggest pain: giant notes, file explosion, merge conflicts, noisy search, performance, something else?

• How often do you revisit raw, uncommented highlights?

• Hidden JSON layer + selective Markdown: feels clean or confusing / opaque?

• Linking preference: block refs inside one note vs separate tiny notes per annotation?

• Any horror stories (5k+ line annotation notes or thousands of micro-files)?

• Which model (1–4) best matches how you actually work—and why?

Huge thanks—I’m leaning heavily on the community’s deeper experience. Even a few bullet points or a rant helps shape the default I ship.

[Sunnaq445]

I am not qualified to answer poll questions but got to say seeing Zotero live inside Obsidian like this looks intriguing!!
Hope this gets more replies.

[moz]

The idea sounds great.

I’m using Zotero to manage PDFs. As a PDF reader, Zotero could handle highlights and notes well. After note taking, I will use a plugin Call Zotlit to migrate the notes, highlights, and metadata(e.g. backlinks) to Obsidian.

Basically, on Obsidian every PDF has its note file. The highlights and notes will display as Callout with a backlink to the source.

May this inspire you something?

[Sunnaq445]

Yesterday I was facing a problem: I wanted a single quote from a book and did not want to read the whole book. But I said no, not gonna highlight and import via the usual means, just copy and paste.

The best part of such plugin (apart from not having to add PDF to vault) would be to take a passage from a source and forget about it and be able to do it again next time this source is needed, without having to do imports and and be wary of what happens on re-imports. Seamless integration.

The PDF++ plugin of course would be a great inspiration. May be you guys could even collaborate although the other plugin developer may not be interested in Zotero.?