How to Convert Obsidian Vault PDFs to EPUB — Read Your Research on Kindle or Kobo
Obsidian is the PKM app of choice for thousands of researchers, writers, and knowledge workers. Many keep research PDFs in their vault alongside their notes. Obsidian's built-in PDF viewer works on desktop — but for reading long papers comfortably, converting to EPUB and reading on an e-reader is far better.
PDFs in Obsidian
Obsidian stores PDFs as local files in your vault folder, alongside your Markdown notes. You can:
- Embed PDFs in notes:
![[paper.pdf]]renders the PDF inline in a note - Link to PDFs:
[[paper.pdf]]creates a clickable link - Annotate PDFs: With the Annotator community plugin, highlight and comment directly in the vault
Obsidian's PDF viewer is excellent for desktop annotation. For mobile reading or e-reader reading, EPUB is better.
Finding your vault PDFs
To find all PDFs in your vault:
- In Obsidian: Press Ctrl/Cmd+Shift+F → search
file:.pdf - In your file manager: Open the vault folder → search for *.pdf
- Common locations: Attachments/, Literature/, Files/, or wherever you drag files when creating notes
To open a vault PDF in your file manager from Obsidian: right-click the PDF in the file explorer panel → Reveal in Finder/Explorer.
Converting to EPUB
- Locate the PDF in your vault folder (Attachments/ or wherever you store files)
- Go to pdf2epub.toolkit.bot
- Upload the PDF
- Wait ~30 seconds
- Download the EPUB
- Transfer to your e-reader: email to Kindle, USB to Kobo, or open in any EPUB app
Obsidian + e-reader reading workflow
| Step | Tool |
|---|---|
| Find and save research papers | Browser → drag PDF to Obsidian vault |
| Initial reading pass (absorb the paper) | EPUB on Kindle, Kobo, or reMarkable |
| Deep annotation and highlighting | Obsidian PDF viewer + Annotator plugin |
| Writing reading notes and connections | Obsidian note linked to PDF |
| Citation and bibliography | Obsidian Citations plugin + Zotero/BibTeX |
Frequently asked questions
How does Obsidian handle PDF files?
Obsidian stores PDFs as local files in your vault folder, just like Markdown notes. You can embed a PDF in a note using [[filename.pdf]] or ![[filename.pdf]], and Obsidian renders it inline using its built-in PDF viewer (powered by PDF.js). The PDF viewer supports basic reading and annotation with the Annotator plugin. However, Obsidian's PDF viewer is designed for desktop use — it doesn't reflow text for small screens.
Where are PDFs stored in an Obsidian vault?
PDFs are stored wherever you placed them in your vault folder — there's no special PDF folder unless you created one. Common conventions: some users put PDFs in an Attachments/ folder, others in a Literature/ folder alongside their reading notes. To find all PDFs, use Obsidian's built-in search with the filter: file:.pdf. Or browse the vault folder on your computer — it's just a regular folder with files.
Can I use Obsidian's annotation features with an EPUB?
Not natively — Obsidian's built-in annotation (via the Annotator community plugin) supports PDFs and web annotations, not EPUB files. The EPUB-to-e-reader workflow is complementary to Obsidian annotation, not a replacement: read the EPUB first on your e-reader for the initial pass, then open the original PDF in Obsidian for deep annotation and linking to your notes.
What is the Obsidian + e-reader reading workflow?
A common workflow: (1) Save a PDF to your Obsidian vault using the 'Attachment' feature or manual copy. (2) Convert the PDF to EPUB at pdf2epub.toolkit.bot. (3) Read the EPUB on your Kindle or Kobo — take light highlights and notes. (4) Return to Obsidian and open the original PDF with the Annotator plugin for detailed annotation. (5) Create a reading note in Obsidian linking to the PDF attachment, capturing key ideas and quotes.
Does pdf2epub.toolkit.bot work with Obsidian's local PDF files?
Yes — you can upload any PDF to pdf2epub.toolkit.bot regardless of where it's stored. Open your vault folder in Finder or Explorer, drag the PDF to the browser upload area at toolkit.bot, and convert. The original PDF remains in your vault untouched. The EPUB is a separate file you transfer to your e-reader — it doesn't need to be in the vault.