How to Connect Obsidian with EBooks

Although the title I use is How to Connect Obsidian with Books, the showcase introduced here can be used in all note-taking software (include Typora, Roamresearch, etc. ) to make at least one-way link between notes and documents, like books–>Typora, Roamresearch, Logseq, etc.


You need at least two softwares(and three plugins btw) to connect books with Obsidian.

Links to download these softwares or plugins are at the end of article.

Next, I will show you how to connect obsidian with books by using these softwares and plugins.



Zotero cooperates with Zotfile to support the extraction of notes or highlights in pdfs, which gives you corresponding positions of those notes or highlights and content of them.

For exmaple, you got a Book.pdf with many notes or highlights, now you import it into Zotero, you will get a item named Book. Then, click the Manage attachment->Extract Annotations in the context menu of the item. Gotcha, you get all notes or highlights of Book.pdf and the positions of them.

You can just copy them on the Notes pane in zotero, but now you have another way to make things perfect. By using Mdnotes, these notes can be transformed into more MD-like notes. Like screenshot as followed.

When you click on any link near these notes, you can jump to positions of the notes or highlights you took. You can jump to the original text to view the context.

PS: Zotero using URI(like obsidian did) to let you jump to specific page. The link it generated seems like

[note on p.?](zotero://open-pdf/library/items/GIBFC4MH?page=5)

PLUS workflow:

  • Copy notes URL to make them a hyperlink that links to the notes or highlights, which means Obsidian<–>Pdf


Calibre is a book manager with a slow opening book viewer, the book viewer supports near all kinds of ebooks on the web.

Before Calibre ver 5.9.0 released, I used it to transfer or manage my ebooks. But release of Calibre ver 5.9.0 makes things change: it allows you to jump to location of the notes or highlights of the book like Zotero( Also like Obsidian)

Use book viewer of Calibre to read book, take notes in it or highlight text in it. Then close the book and press B key on your keyboard, select the Export all selected in the lower right corner of the panel (Sorry I was using CN-GUI)

A pop-up menu will let you choose what format to export or copy directly to the clipboard.

Finally, you get all your notes on your books as follow.

Just enjoy jumping from notes to ebooks.


If you ever tried zettelkasten or read how to take smart notes , you do know how important for people to take literature notes. Notes with a jump-able link are helpful for people to read context or trace to the source.


Some methods or techniques have been shared in the forum, I just did a small job of integrating these techniques or methods. Hope these would be helpful for you.


Thanks for sharing. I’ll just add that further features have been added to calibre in recent versions, such as having a link export button in the toolbar. The dev is somewhat prickly, but is generally quite open to feature requests.

Thanks for telling me about this.

Note also that epub books are just plain old HTML in a zip file.

I tend to unzip mine and then manually convert them to MD for obsidian. This does take some time (you could use pandoc, but I havent figured out how), but it means that I do both my reading and note taking in obsidian.


That’s very intriguing… Do you convert them to a single Md file? Different ones for each chapter? Does it maintain formatting? What about pictures?

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I don’t recommend my workflow :rofl: unless you have a specific need like mine (I tend to spend a lot of time on a single book, so it balances out):

  1. Right click epub > extract (you may need to rename to .zip, or use 7zip)
  2. Create an index page in obsidian, copy and past the TOC page
  3. For each chapter, create a page, link from TOC page
  4. For each chapter, copy and paste into obsidan
  5. Find and replace all epub links with obsidian links

When it comes to referencing, then I just hit [[^^ to find the paragraph.

Picture are usually in the “resources” folder, so I just use ![[ to inline these.

Re. Formatting, most of my books (corporate strategy, philosophy and psychology) comes across just fine, however, textbooks do not - I haven’t figured this out yet…


Thanks! I’ll stick with Ebooks in calibre and its annotations and URL links.

I think,we can convert epub to PDF via Calibre and then convert PDF to MD via Obsidian’s PDf to MD plugin.

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I did same conversion by using calibre. And then read the book in Obsidian.

This is very interesting! Did you convert the book into Markdown? Can you be more specific about this how to do this in calibre?

It would be interesting to be able to read the book directly in Obsidian. Then one can easily write literature notes and block link to specific locations in the book.