How to Export Logseq Notes and PDFs to EPUB — Read Your Graph on Kindle or Kobo
Logseq is a privacy-first, local-first knowledge base used by researchers, writers, and knowledge workers worldwide. It stores PDFs in a local assets folder and has a built-in PDF viewer for annotation. For comfortable reading of long papers, converting to EPUB and using an e-reader is significantly better than reading on screen.
PDFs in Logseq
Logseq handles PDFs in two ways:
- PDF attachments: Drag a PDF into any Logseq page — it's stored in the
assets/folder and embedded inline. The built-in viewer supports text highlighting and comments saved as block references. - Linked PDFs: Reference any PDF file on your system using a local file link.
The built-in PDF viewer is useful for annotation. For reading long papers comfortably, EPUB on an e-reader is better.
Finding assets in your graph
All dragged-in PDFs live in the assets/ folder of your graph:
- Open your file manager and navigate to your Logseq graph folder (wherever you created the graph, e.g.
~/Logseq/my-graph/) - Inside, open the
assets/folder — all PDFs are there - Or: in Logseq, right-click an embedded PDF → Open in Default App — this opens the PDF and reveals its location
Converting to EPUB
- Find the PDF in your
assets/folder - 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 reading app
Exporting Logseq notes as EPUB
To export your Logseq notes (not source PDFs) as EPUB for reading:
- Open the Logseq page containing your notes
- Click the ⋯ menu → Export → PDF
- Upload the exported PDF to pdf2epub.toolkit.bot
- Convert to EPUB and read your research notes on your e-reader
This is useful for reading long research summaries, project documents, or compiled reading notes.
Logseq + e-reader workflow
| Task | Best tool |
|---|---|
| Save papers and clip references | Logseq + drag PDF into page |
| Initial reading pass | EPUB on Kindle, Kobo, or reMarkable |
| Detailed annotation and highlights | Logseq built-in PDF viewer |
| Bidirectional note-linking | Logseq block references and [[page links]] |
| Bibliography and citation | Logseq Zotero plugin or manual reference blocks |
Frequently asked questions
How does Logseq handle PDF files?
Logseq stores PDF attachments in an 'assets/' folder within your graph directory. You can embed PDFs in any page using the ((embed)) syntax or by dragging a PDF into a note. Logseq renders PDFs inline using a built-in viewer that supports basic annotation — highlight text and add comments that are saved as block references in your graph. The viewer works on desktop but is designed for annotation, not comfortable long-form reading.
Where are PDF attachments stored in a Logseq graph?
Logseq stores attached PDFs in the 'assets/' folder inside your graph directory. The graph directory is wherever you created your Logseq graph — typically ~/Logseq/[graph-name]/ or a folder you chose during setup. Within that folder, look for assets/ — all dragged-in PDFs, images, and other attachments are there. You can also right-click any embedded file in Logseq → Open in Default App → which reveals the file location.
Can Logseq export pages to PDF?
Yes — Logseq can export individual pages or your entire graph to various formats. To export a page to PDF: open the page → click the three-dot menu → Export → PDF. This creates a PDF of the page content (your notes, not the embedded source PDFs). For converting your Logseq research notes to EPUB for e-reader reading, export them to PDF first, then convert at pdf2epub.toolkit.bot. Note: this exports your notes about papers, not the source PDFs themselves.
What is the difference between Logseq and Obsidian for PDF reading?
Both are local-first knowledge management tools that store PDFs in a local folder and have built-in PDF viewers. Logseq uses a daily notes / outline approach with bidirectional links; Obsidian uses a Markdown file approach. Logseq's PDF annotation saves highlights as block references directly in your graph — tight integration. Obsidian uses the Annotator plugin for similar functionality. For EPUB conversion and e-reader reading, both work identically: locate the PDF in the assets/ or attachments/ folder, upload to pdf2epub.toolkit.bot, convert.
Can I use Logseq highlights after converting to EPUB?
Logseq's PDF highlights are stored as block references in your graph (in the .logseq/ folder or as page references), not inside the PDF file itself. They won't appear in the EPUB. The EPUB is for the initial reading pass — use it to absorb the paper before doing detailed annotation. After reading the EPUB, open the original PDF in Logseq for annotation and note-linking. Many researchers use both: EPUB for first read, Logseq PDF viewer for annotation.