Working with scientific literature mostly relies on PDFs. However, for a lot of domains, electronic books are much more useful. The question I get asked a lot is: How do you work with EPUBs and Kindle annotations? Here’s the exact workflow.
Learn the foundational systems researchers are rarely taught: from powerful note-taking and knowledge management methods to modern lit review tools, ethical AI and productive research workflows.
This setup only makes sense if you are using Obsidian as your note-taking and second brain app. If you don’t, head over to absolute beginner Obsidian tutorial first, then come back here. Here is what a typical note on a book with an imported Kindle highlight looks like in my vault:
There are effectively three ways to connect your eReader to Obsidian: ReadWise Sync (Premium solution for 10$/mo), Unearthed (13$ one-time purchase), and various Kindle Importer plugins (free). I’ve tried all of them and settled on using Unearthed for over a year now. Let’s dive into them.
How do you get Kindle highlights into Obsidian?
There are three good ways to move Kindle annotations into your vault. Each one trades cost against convenience, so the right choice depends on how many books you read and how much manual work you are willing to do. My suggestion is to go with Option 2, as it is cheap and powerful.
Method 1: Readwise and the Readwise Obsidian plugin
Readwise syncs your Kindle highlights automatically, and its official Obsidian plugin drops them straight into your vault. It works well and has the most flexibility when pulling data from the book. You first create an account with Readwise and configure all export settings online. The official Obsidian plugin syncs everything in the background.
Readwise also gives you the most control over how highlights arrive. Its import template exposes far more variables than any other method, so you can shape the title, metadata, tags, note structure, and even conditional formatting exactly how you want. If you care about your book notes matching a precise layout, this is the most flexible option available.
The catch is the price. Readwise costs $10 per month. I used to pay for it, but for the number of books I import it was too expensive to justify an ongoing subscription. If you also use Readwise for articles, newsletters, and web highlights, the cost makes more sense. For Kindle alone, it is a lot.
Method 2: Connect Obsidian to Kindle with the Unearthed app
Unearthed has become my best solution for working with Kindle books. It is a small app that runs locally on your computer in the background and pulls your Kindle annotations straight into your local Obsidian vault. The app also supports RSS feeds, YouTube videos, and even physical books (using a mobile app, I developed my own workflow for this):
My suggestion is to use Unearthed Local, which is stand-alone software that costs $13 (one-time, not a subscription). Unearthed only syncs on one machine. That sounds like a limitation, but if your vault uses Obsidian Sync or another sync service, the imported notes propagate to every other device anyway. The app writes to one vault, and sync carries the rest. Importantly, Obsidian does not need to run in order for the synchronization to happen, as Unearthed writes directly into your Obsidian vault.
Since this is the workflow I really recommend, I will go into detail on setting it up in the next section.
Method 3: Manual Kindle highlight importer plugins
There are several community plugins that read your Kindle highlights and import them into Obsidian, and most of them are free. The best-known is the Kindle Highlights plugin by hadynz. It runs a search across your Kindle library, identifies each book and its highlights, and pulls them in either through your Amazon login or by reading the My Clippings.txt file straight off the device over USB. It even supports flexible templating, so the notes can be shaped to your liking.
The reason why I don’t use these is typically a lack of options and configurations and generally a clunky UI to configure the templates. For instance, including/excluding certain books from synchronizing in Kindle highlights requires you to look up the exact title and type it in, which is a really tedious trial-and-error process.
However, if you are just starting out, try this plug-in first to understand which features you actually need before paying for a premium solution.
How to set up Unearthed for Kindle and Obsidian
Setup takes a few minutes. Here is the exact process.
1. Download and install the app. Download it from the Unearthed site (13$ one-time payment) and install it like any other desktop application.
2. Connect it to your Amazon account. You log in with your Amazon credentials so the app can read the highlights tied to your Kindle library. The app will guide you through it.
3. Set the import location. You point Unearthed at your vault and choose the folder where your source notes should land. This keeps all your book notes in one predictable place. Keepin mind that Unearthed will create subfolders in the “Root folder” (e.g. “Books”):
4. Set up the import template. You define how each imported note is structured using a handful of variables: title, subtitle, author, type, origin, and ASIN for the source note and {{content}}, {{note}}, {{location}}, {{color}} for individual highlights. Here is my configuration:
Since I have an older Kindle, I disabled highlight colors. This is, however, relevant if you read on your computer (using the Kindle app), where the colors can be useful.
That is the whole setup. Once the template is saved, your Kindle highlights appear in your vault automatically because Unearthed writes directly to the vault folder, whether Obsidian is running or not.
Suggestion: Sync only the books you are currently reading
The source notes that Unearthed provides are typically not perfect due to missing variables (e.g., no cover image) or metadata that doesn’t quite suit you (e.g., a title that is too long to be practical). If you change these things while Unearthed is actively syncing it, you may often create duplicate data (if you change the title), or Unearthed might overwrite the content (if you change the source note contents).
My solution: After finishing the book, I take the note created by Unearthed and put it in a different folder. I also added this book to Unearthed’s ignored list so it’s no longer synchronized. This is also the part where I will start engaging with the highlights and linking them to my vault. This protects your source notes from being accidentally overwritten.
Using this method, you have to touch the Unearthed app only once you’re finished with the book, which probably doesn’t happen too often.
Other Unearthed features worth knowing
Unearthed has a few extra editions and modes. A nice one pulls a random old highlight into your daily note, so you get reminded of something you highlighted maybe years ago. It is a simple way to keep past reading in circulation instead of letting it rot in a folder.
The RSS and YouTube import feature also overlaps with browser-based capture. If you want to pull web content into Obsidian as well, the WebClipper plus AI workflow pairs nicely with it.
How do you take notes on physical books in Obsidian?
Unearthed is a great addition to a Kindle setup. But plenty of the best non-fiction is read on paper, and physical books need a different workflow.
I wrote a full walkthrough for this: how to take notes on printed non-fiction books in Obsidian. It covers the source note, the annotation template, a QuickAdd automation, and how to photograph and name pages so they line up with your notes. Here is what my vault looks like once that system is running.
The most important part: Use your annotations for learning, synthesis, and new ideas
Importing highlights is only half the job (the easier half). A pile of quotes in a folder does nothing for your learning. You will not remember them, and you certainly will not use them when you sit down to write. For your notes to be useful, you must connect them to your knowledge network. Here is my workflow:
1. Use AI to surface relevant connections to begin
After I finish a book, I run a “Cross Reference” Claude skill that analyzes the highlights and my vault, finds notes related to the book, and links them at the top of the file (or just prints them out). One alternative is to use the Smart Connections plugin, which is faster but gives you merely a list of notes. This does the hard part of memory for you. Instead of trying to recall which old notes a book relates to, the vault hands you the candidates, and you decide which connections are real. A new book lands inside your current thinking rather than sitting in a folder you never reopen.
To enable this workflow, you need to configure an agents.MD file (see this tutorial), which tells your AI exactly where to look for the relevant notes. Different models will give you different results. I really like the Google Gemini Scribe plugin because it is often more thorough when searching my vault. Here is my prompt:
Given the attached note, understand the concept it deals with and find related ideas in my notes. Create an output which links them to my note that I could add to the note. Also add a few provocative questions you can come up with.
Finally, find areas in my vault (especially root notes) where this article can contribute something meanigful and describe what this contrubution could be.It’s often best not to just copy-paste from AI, as that doesn’t really help your understanding either. Engage with the highlights and do the work manually. Learn.
2. Capture claims with block links
Following the same system I use for academic notes, I try to extract the claims the book makes and back them up with highlights from the Kindle. Technically, this is done by creating so-called block links that let you point to a single line or passage inside another note rather than the whole file. You write the claim in your own words, then link it straight to the exact sentence in the book that supports it. The copy block links plugin makes linking to blocks easier.
Using this method is very similar to the PDF++ workflow I use for academic papers.
3. Why the network matters: three real use cases
The effort pays off the moment you need to use what you read.
- Writing a paper or essay. Every claim you make already carries a link back to the passage that justifies it, so you never lose the evidence trail or spend an afternoon hunting for the book a quote came from.
- Connecting ideas across books. When a note about “climate change” links to three different authors who touched on the same theme, you can see the disagreement between them at a glance. That tension is often where your own original thinking starts.
- Remembering across time. Months later, when you open an old note for an unrelated project, the linked book idea shows up beside it and reminds you of something you would otherwise have forgotten. The network keeps past readings in circulation.
- Books are grounded in existing knowledge. Using the backlinks of the source note, you can instantly identify which books deal with which topics, making it easier to remember them.
If you also work with annotated PDFs, the same linking approach applies with the PDF++ plugin in Obsidian, and the broader note-taking hacks for academics build on the same idea.
Kindle highlights in Obsidian: common questions
What is the easiest way to save Kindle highlights into Obsidian?
The easiest way is the Unearthed app. It is a one-time $13 purchase that runs locally in the background and syncs your Kindle highlights into your vault automatically, with no monthly subscription and no manual imports to babysit.
How do you export Kindle highlights to Obsidian?
There are three ways to export Kindle highlights to Obsidian: the Readwise plugin (automatic, subscription), the Unearthed app (automatic, one-time payment), or a free community plugin that reads your My Clippings.txt file or your Amazon login. Readwise and Unearthed keep highlights in sync, while plugins import them manually.
Can you convert Kindle highlights to Markdown?
Yes. Every method here writes your Kindle highlights as plain Markdown notes inside your vault, so they become searchable, linkable, and editable like any other note. Nothing stays locked in a proprietary format.
Is there an Obsidian Kindle highlights template you can customize?
Yes. Unearthed, Readwise, and the Kindle Highlights plugin all use editable templates. You control the layout with variables such as title, subtitle, author, type, origin, and ASIN, and Readwise exposes the largest set of variables if you want the most detailed formatting.
Do you need an Obsidian Kindle highlight plugin?
No. With Unearthed you do not need a plugin at all, because the app writes highlights straight into your vault from outside Obsidian. A plugin is only required if you prefer the manual My Clippings route through the Kindle Highlights plugin.
Summary
If you read on a Kindle, getting your highlights into Obsidian no longer needs to be a chore.
► Readwise is the most automatic and the most flexible on formatting, but the $10 per month adds up if Kindle is all you use it for.
► Unearthed is my pick: a one-time $13 app that runs locally, syncs only the book you choose, and now imports RSS and YouTube channels too.
► Manual importer plugins like the Kindle Highlights plugin are free but lack customisation and can risk overwriting your own notes.
► The real value comes after import: link each book to related notes and use block links to tie every idea back to the exact passage that supports it.
Highlights are only useful when they connect to the rest of your thinking. Set up the import once, then spend your energy on the linking, which is where reading actually turns into knowledge.
