Kobo Export Not Working? Every Fix That Actually Works

If you connected your Kobo, went looking for an export or backup option, and came away with nothing — or an export file missing most of your highlights — you are not doing anything wrong. The official export feature has real, documented limitations. This guide explains exactly why it fails, then compares every workaround honestly so you can pick the one that fits how technical you want to get.

Why Kobo's official export fails

Kobo stores every highlight, note, and bookmark in a single file on the device called KoboReader.sqlite — a SQLite database. The device's own export feature reads from this database, but it was built around Kobo Store purchases and has two well-known gaps:

  • Sideloaded books are excluded. If you added an EPUB or PDF to your Kobo yourself — from a library loan, a personal PDF, or a book bought outside the Kobo Store — the official export pipeline frequently skips it entirely, even though your highlights for that book are sitting in the same database file as everything else.

  • Long highlights get truncated. Passages you highlighted in full can come back cut off partway through in the exported file, losing the context that made the passage worth marking in the first place.

Neither of these is a sign of data loss. The full highlight text and every sideloaded book's annotations are still stored in KoboReader.sqlite — the problem is entirely in how the official export reads and formats that data, not in what Kobo recorded.

Every workaround, compared honestly

1. Kobo's official export

Best for: readers whose entire library is Kobo Store purchases with short highlights. Downsides: skips sideloaded books, truncates long highlights, and offers no control over the output format.

2. Calibre with a Kobo highlights plugin

Best for: readers who already manage their library in Calibre and don't mind installing a desktop app plus a community plugin. Downsides: requires installing and maintaining two separate pieces of software, and plugin quality/format support varies by which one you pick.

3. Manually querying KoboReader.sqlite

Best for: developers comfortable with a terminal who want full control over exactly what gets extracted. Copy KoboReader.sqlite off the device, open it with any SQLite client, and query the Bookmark table directly. Downsides: requires SQL knowledge, a SQLite client, and manually mapping content IDs back to book titles — not realistic for most readers.

4. Kobo Note Up (browser-based, no install)

Best for: anyone who wants sideloaded books included and full highlight text preserved, without installing anything. How it works: it opens KoboReader.sqlite directly inside your browser tab using SQL.js, a WebAssembly build of SQLite, and reads every highlight from every book the same way — Kobo Store or sideloaded. Nothing is installed on your computer, and by default nothing is uploaded anywhere: the file is parsed entirely on your device. The honest tradeoff is that it's a newer, smaller project than Calibre, so it does one job (reading and exporting highlights) rather than Calibre's much broader library-management feature set.

Step-by-step fix using Kobo Note Up

  1. Connect your Kobo e-reader to your computer with a USB cable. It will mount as a normal removable drive.

  2. Open Kobo Note Up in Chrome, Edge, Firefox, or Safari.

  3. Chrome or Edge: select your Kobo's root drive folder directly when prompted. Firefox or Safari: these browsers cannot read a USB drive's root folder, so select the .kobo folder inside your Kobo device instead. That folder is hidden by default — on Mac, press ⌘+Shift+. while the file picker is open to reveal it; on Windows, enable "Show hidden files" in folder options, or use the Ctrl+H trick some file dialogs support.

  4. The tool automatically finds KoboReader.sqlite and lists every book, sideloaded or not.

  5. Open any book to see its full, untruncated highlights and notes, and export the whole library or individual books to Markdown.

Frequently asked questions

Why does my Kobo export button do nothing, or export an empty file?

Kobo's built-in export (My Kobo → Export annotations, or similar menus depending on firmware) only reads highlights from books bought through the Kobo store. If your library is mostly sideloaded EPUBs or PDFs, the export can look like it did nothing because it genuinely found nothing to export from those books.

Will any of these methods damage my Kobo or my highlights?

No, as long as you only read from KoboReader.sqlite and never edit it while your Kobo is running its own software. Official export, Calibre, manual SQLite queries, and Kobo Note Up all read the database without writing to it, so your device and existing highlights stay untouched.

Do I need to know SQL to get my highlights out?

No. Running a manual SQLite query is one valid workaround, but it requires comfort with a terminal and basic SQL. Calibre and Kobo Note Up both give you a normal point-and-click interface instead.

What if my highlights are still truncated after switching tools?

Truncation is specific to Kobo's own export pipeline, not to the underlying database — the full highlight text is always stored in KoboReader.sqlite. Any tool that reads the database directly, including Calibre plugins and Kobo Note Up, will show the complete text.

Related guides

Ready to get every highlight out, including the sideloaded books Kobo's own export ignores? Try Kobo Note Up now — it's free, open source, and runs entirely in your browser.