Export Kobo Highlights to Markdown for Obsidian

Obsidian is just a folder of Markdown files on your computer, which makes it one of the easiest places to land Kobo highlights — there's no import wizard or special format to learn, you just need a well-structured .md file. This guide covers where your highlights actually live on the Kobo device, how to get a browser to see them even on Firefox and Safari, and exactly how the export drops into a vault.

Where KoboReader.sqlite lives on each OS

Every highlight, note, and bookmark on a Kobo device is stored in one SQLite database file, KoboReader.sqlite, inside a hidden .kobo folder at the root of the device's drive. After connecting your Kobo via USB, you'll typically find it at:

  • Windows: E:\.kobo\KoboReader.sqlite (the drive letter depends on your system)

  • Mac: /Volumes/KOBOeReader/.kobo/KoboReader.sqlite

  • Linux: /media/[username]/KOBOeReader/.kobo/KoboReader.sqlite

You don't need to navigate to this path by hand — Kobo Note Up scans for the file automatically once you point it at the device. The paths above are useful mainly for understanding what's happening, or if you want to inspect the database with your own tools.

Hidden-folder tips for Firefox and Safari

Chrome and Edge can open a USB drive's root folder directly and let Kobo Note Up find the database on its own. Firefox and Safari don't support that browser API, so they'll show an empty or unreadable folder if you select the drive's root. The fix is to select the .kobo folder itself, one level in — but that folder is hidden by your operating system by default, so you need to reveal it first:

  • Mac: in the file picker, press ⌘+Shift+. (Command, Shift, period) to toggle hidden files on, then navigate into .kobo.

  • Windows: enable "Show hidden files" in File Explorer's folder options before opening the file picker, or try the Ctrl+H shortcut some file dialogs support for the same toggle.

Once .kobo is visible and selected, Kobo Note Up reads KoboReader.sqlite from inside it exactly the same way it would from a root-folder selection.

Step-by-step: exporting to Markdown

  1. Connect your Kobo to your computer via USB.

  2. Open Kobo Note Up and select your Kobo's folder — the root folder in Chrome/Edge, or the .kobo folder in Firefox/Safari as described above.

  3. Browse the list of books the tool finds — sideloaded and Kobo Store purchases alike.

  4. Open a single book and choose "Download as Markdown" for just that book, or use the library-wide export to download every book as a ZIP of separate Markdown files, or as one combined Markdown file.

Each exported file starts with the book title as a top-level heading and the author as a second-level heading, followed by your Kobo chapter structure. Highlights appear as bullet points — with a colored emoji marker if you used Kobo's highlight colors — and any notes you attached appear as Markdown blockquotes directly under the highlight they belong to.

Getting the file into Obsidian

Because Obsidian vaults are just folders on disk, there's no dedicated "import" step: move or save the exported .md file(s) into any folder inside your vault (via Finder, File Explorer, or Obsidian's own file explorer), and it appears in Obsidian's sidebar immediately. The headings become that note's outline, and each highlight/annotation pair reads as a normal bullet with a quoted note beneath it — no plugin or special formatting required. If you'd rather review everything in one file, use the combined-library export instead of the per-book ZIP and Obsidian will treat it as a single long note.

Frequently asked questions

Where exactly is KoboReader.sqlite stored?

It's on the Kobo device itself, inside a hidden .kobo folder at the root of the drive. When connected via USB it typically shows up at E:\.kobo\KoboReader.sqlite on Windows (drive letter varies), /Volumes/KOBOeReader/.kobo/KoboReader.sqlite on Mac, and /media/[username]/KOBOeReader/.kobo/KoboReader.sqlite on Linux.

Why can't Firefox or Safari see my Kobo's root folder?

Firefox and Safari don't support the browser API (the File System Access API) that lets Chrome and Edge open a USB drive's root folder directly. They can still read files you explicitly pick, so the fix is to navigate one level deeper and select the .kobo folder itself, which those browsers can open.

Do I need to install an Obsidian plugin to use the exported file?

No. The export is a plain .md file using standard Markdown headings, bullet points, and blockquotes. Obsidian reads any Markdown file placed inside its vault folder with no plugin required.

Does the exported Markdown preserve highlight colors and handwritten notes?

Highlight colors are preserved as emoji markers next to each highlight. Handwritten annotations from a Kobo stylus are noted in the Markdown text; the full annotation image itself is available through the Notion export path rather than the Markdown export.

Related guides

Ready to export? Open Kobo Note Up — free, open source, and it never uploads your database during a normal Markdown export.