How to Take Notes in PDFs & EPUBs in Obsidian(Highlighting & Annotations)

Obsidian can turn PDFs and EPUBs into a full note-taking workspace by letting users highlight text inside the document and attach annotations that automatically appear as saved notes in Obsidian. The workflow matters because it eliminates the need for separate e-reader apps (or Kindle-style ecosystems) when someone wants to read on a laptop or mobile and keep highlights organized for later retrieval.

The process starts with installing an Obsidian community plugin named “annotator.” After enabling community plugins in Obsidian’s settings, users browse for “annotator,” install it, and then open the plugin options. Key configuration includes turning on annotation mode by default so highlights can immediately generate note entries. The setup also includes optional formatting behaviors: prefix/postfix settings can automatically add extra text around highlights in the resulting notes, and the creator recommends turning those off. There are also display-related options such as dark mode and color choices; light mode is used in the walkthrough.

Once the plugin is configured, users create a new note in Obsidian and add metadata that points to the target document. For local files already stored in the Obsidian vault, the note uses the full filename (including the file extension) as the annotation target. For documents stored in remote storage, the note can instead reference a path to the EPUB/PDF; the plugin then opens the file through that remote link. In either case, the “annotate” option is used to open the document within Obsidian.

Inside the opened PDF/EPUB, selecting text enables highlighting. Each highlight can be followed by an annotation step: users add a note (for example, an idea or question) and then post it so it becomes a persistent annotation entry. These entries can be organized and browsed by newest/oldest and by location within the document, with the walkthrough showing that highlights are tracked by their last highlighted location.

After annotations are created, switching to editing versus reading mode changes how they appear. In editing mode, the annotations show up in a more raw markdown-like structure, while reading mode previews the notes in a block-code style format (with styling controlled by CSS). For review, the plugin supports “show annotation,” which jumps directly back to the corresponding location in the PDF/EPUB where the highlight occurred. The net result is a searchable, linkable system for highlights and notes that stays inside Obsidian, suitable for readers who want a single platform for long-form reading and future reference.