PDFs in Your Notes App: Convert to EPUB for Reading — Obsidian, Evernote, OneNote and More
Whether your reading lives in an Obsidian vault, an Evernote notebook, a OneNote section or a DEVONthink database, the problem is the same: the PDF is fine for annotating at a desk and miserable to read on a phone or e-reader. Convert it to EPUB, read it on a Kindle or Kobo, and bring the highlights back to your notes. This guide starts with Obsidian — the vault is a plain folder, so it is the easiest case — then covers where eleven other notes apps keep their PDFs and how to get one out.
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 |
Other notes apps: where the PDF lives and how to get it out
The conversion step is identical for every app — upload the PDF, download the EPUB. What differs is where the app keeps the PDF and how you get a copy onto disk. Obsidian is easy because the vault is a folder; the rest are below.
| App | Where the PDF lives | How to get the PDF out |
|---|---|---|
| Evernote | Attachment inside a note | Desktop: right-click the attachment → Save Attachment. Web: click the PDF preview → download. iOS: tap → share → Save to Files. Android: long-press → Download. Each attachment is exported separately. |
| OneNote | Attachment icon on a page — or the notes themselves | Attachment: right-click the icon → Save As. To read your own notes as an ebook: File → Export → Page, Section or Notebook → PDF. Section names become chapters. Run Ink to Text on handwriting first, or it exports as images. |
| Roam Research | PDF embeds in a cloud graph; no local file store | Keep the original file you downloaded (arXiv, PubMed, your Downloads folder) and convert that. Roam is the destination for highlights, not the PDF store. |
| DEVONthink | Record inside a DEVONthink database (Mac) | Right-click → Reveal in Finder, or drag the record to the desktop. DEVONthink 3 reads EPUB natively: drag the converted EPUB back into the same group and it stays indexed, searchable and linked by See Also & Classify. |
| Heptabase | Uploaded to a card or whiteboard | Use the original download; Heptabase's built-in PDF annotator is for desktop work. Highlights come back as bullet points in a card for the paper, placed on your literature-review whiteboard. |
| RemNote | Uploaded to a document (browser PDF viewer) | Use the original download. RemNote imports PDF and text, not EPUB — the EPUB is for the e-reader, RemNote is for turning highlights into flashcards. |
| Tana | No PDF viewer or file store | Use the original download. Highlights arrive through the Readwise → Tana integration as nodes you tag with a #paper supertag. |
| Capacities | File attachment on a Book or Article object | Download the attachment from the object, or use the original file. No built-in reader; highlights sync via Settings → Integrations → Readwise. |
| Craft | Embedded file block in a document | Open the file block and save the PDF, or use the original. Craft has no annotation layer; bring highlights back as text blocks or a Markdown import. |
| Bear | Attachment inside a note (Apple devices) | Tap or click the attachment → share or save it. Bear has no PDF annotation; paste highlights into a note tagged with your project. |
| Scrivener | Your draft is not a PDF yet — compile it | File → Compile → PDF with a simple preset (Default or Novel) and a page break before each chapter. Convert the compiled PDF and proofread the draft on an e-reader; the chapter headings become the EPUB table of contents. |
Zettelkasten and other reading-first methods
If you keep a Zettelkasten — one atomic idea per note, linked to its source — the app matters less than the order of operations: read and highlight first, write Zettels second. Highlighting a two-column paper as a PDF often mis-selects text across columns; the EPUB is linear, so highlights capture exactly the passage you chose and export cleanly to Obsidian, Logseq, Roam or Notion.
Getting highlights back into your notes app
The EPUB is a reading copy; your notes app is where the highlights end up. Readwise is the usual bridge — it collects highlights from Kindle, Kobo, Apple Books and Readwise Reader, then pushes them on:
- Native Readwise integration: Obsidian (official plugin), Roam Research, RemNote, Tana, Capacities, Notion, Logseq
- Markdown export, then paste or import: Bear (Import from Files), Craft (Markdown import), Heptabase (paste into the paper's card)
- Import as a note next to the source: DEVONthink — a Readwise Markdown export becomes a text note in the same group as the PDF and EPUB
- Without Readwise: Kindle highlights are in
My Clippings.txtover USB; a Kobo exports a book's highlights to a file you copy off over USB; Apple Books highlights go through the Share sheet to Bear, Craft or Apple Notes
Scrivener is the exception: the highlights are not notes but passages to fix. Work through them in the manuscript, then discard the EPUB.
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.
How do I get a PDF out of Evernote or OneNote?
Evernote: open the note, right-click the PDF attachment and choose Save Attachment (desktop), click the preview and download (web), or tap → share → Save to Files (iOS). OneNote: right-click the attachment icon → Save As. To read your OneNote notes themselves on an e-reader, use File → Export, pick Page, Section or Notebook, and choose PDF — each section becomes a chapter in the EPUB. Then upload the PDF to pdf2epub.toolkit.bot.
Can I get my Kindle or Kobo highlights back into my notes app?
Yes. Readwise syncs highlights from Kindle, Kobo, Apple Books and Readwise Reader and pushes them natively to Obsidian, Roam Research, RemNote, Tana, Capacities, Notion and Logseq. For Bear, Craft and Heptabase, export from Readwise as Markdown and paste or import. For DEVONthink, import the export as a note in the same group as the source. Without Readwise, Kindle highlights are in My Clippings.txt over USB and Apple Books highlights share to Bear or Craft via the Share sheet.
Does this work for a Scrivener draft?
Yes, and it is a popular proofreading technique. In Scrivener choose File → Compile → PDF with a simple preset (Default or Novel) and a page break before each chapter, then convert the compiled PDF at pdf2epub.toolkit.bot. Read the EPUB on a Kindle or Kobo as a reader would, highlight awkward passages, and fix them back in Scrivener. Inline annotations and comments are excluded from the PDF compile by default, so the EPUB contains only manuscript text.
Which notes apps can read the converted EPUB directly?
DEVONthink 3 has a native EPUB viewer with adjustable font size, and indexes EPUB text for search and See Also & Classify. Evernote displays EPUB attachments inline but without font controls or chapter navigation. Capacities, Craft and Bear store an EPUB as an attachment and open it in an external app. Obsidian, Roam, Heptabase, RemNote and Tana do not read EPUB; for all of them the e-reader is the reading layer and the app is where the highlights land.