Building a second brain for books: Obsidian and Notion workflows vs a dedicated reading app

If you are into personal knowledge management, you have probably built, or at least admired, a book-notes system: a template for each book, literature notes linked to permanent notes, a graph view that lights up as ideas connect. Done well, it turns reading into a body of thought you can draw on for years.

Done in practice, many of those vaults hold a handful of beautifully templated books and dozens of empty ones. This piece looks at why the classic Obsidian and Notion workflows stall for readers, and at a lighter split: let a reading app own capture and recall, and keep your PKM tool for the part it is genuinely best at—synthesis.

The classic book-notes workflow

Most PKM book workflows borrow from the same few ideas: the Zettelkasten tradition of literature notes and permanent notes, and Tiago Forte’s progressive summarization. In practice it looks something like this:

1. Create a note for each book from a template: title, author, dates, status, rating, tags.
2. While reading, collect highlights and page references as literature notes, ideally rephrased in your own words.
3. After reading, distill in layers: bold the key passages, highlight the best of the bold, then write a short summary at the top.
4. Extract permanent notes—one idea each, written to stand alone—and link them to related ideas from other books.
5. Browse backlinks and the graph to find connections, and write from there.

In Obsidian this lives in local Markdown files with backlinks and community plugins; in Notion it lives in a database with properties, relations and views. Both can hold a great system.

The appeal is real. Writing ideas in your own words forces understanding, and linking them across books is where original thinking tends to start. The trouble is rarely the method; it is everything that has to happen before the method can begin.

Where it breaks for readers

The theory is sound. The friction is in the parts that happen away from the desk.

• Capture friction from paper. These tools assume text arrives as text. A paper book means photographing, transcribing or retyping each passage, then pasting it into the right note. In a busy week, that step simply doesn’t happen.
• No review loop. Notes go in and rarely come back. Backlinks help you find connections when you are already writing; they don’t bring last month’s idea back on their own. Spaced repetition plugins exist, but they are another system to set up and tend.
• Templates rot. The template you designed for your first ten books doesn’t fit the eleventh. Properties go unfilled, tags multiply, and old notes follow a scheme you no longer use.
• Maintenance becomes the hobby. Tweaking dashboards, plugins and folder structures is satisfying, and it quietly replaces reading and thinking.

None of this means Obsidian or Notion is the wrong tool. It means one tool is being asked to do three jobs—capture, recall and synthesis—and the first two are the ones that fail silently.

The thin-layer approach

The alternative is to split the jobs by what each tool does best. A reading app owns the parts that need to be quick and habitual: capturing from the page, filing by book and chapter, and bringing notes back on a schedule. Your PKM tool owns the slow part: connecting ideas across books and writing them out in your own words.

The key rule is that nothing moves automatically. Only ideas that survive review make it into the vault, and you move them by hand, rewriting as you go. That rewrite is the synthesis step progressive summarization is trying to encourage anyway; the thin layer just makes sure it happens on ideas you have already met twice.

A useful way to see the split:

• The reading app owns capture: getting a passage off the page and into text within seconds of reading it.
• The reading app owns recall: bringing notes back on a schedule so you meet each idea again before it fades.
• The PKM tool owns synthesis: linking ideas across books, arguing with them, and turning them into your own writing.

Each tool then does less, and does it better. Your vault stops being an inbox, and your reading app never has to pretend to be a writing environment.

A concrete split: GleanNote plus Obsidian or Notion

Here is how the split looks week to week.

1. While reading, capture in GleanNote. Photograph a page and select the lines, or type a highlight. File it under the book and chapter, and add a one-line comment about why it matters. It takes seconds and works offline.
2. Every day, let the Daily Digest bring back a few notes. Read each one in its chapter context. If an idea still feels important, add a word to the comment; if it feels flat, let it go.
3. For facts you want on call, build flashcards from your notes and tap Start review for a few minutes. Most notes won’t need this.
4. Once a week, open your vault and move over only the ideas that survived. Write each one as a permanent note in your own words, and link it to what you already have.
5. When you write, work in Obsidian or Notion, where your synthesized notes and links live. With Premium, Talk to your Book can help you find what you captured about a theme before you start.

The result is a vault with fewer, better notes. The reading app holds the raw material and keeps it circulating; the PKM tool holds only what you have decided is worth keeping.

DIY PKM vs a dedicated reading app

When the all-in-one vault still makes sense

The split isn’t for everyone. If you read mostly digital text that clips straight into your vault, capture friction is low. If you enjoy building and tending your system, the maintenance is part of the value rather than a cost. And if you write for a living from your notes, keeping everything in one linkable place may outweigh the review loop you give up.

The thin layer helps most when you read paper books, when your vault has more empty templates than finished ones, or when you notice you rarely see a note again after you file it.

Frequently asked questions

Is Obsidian or Notion better for book notes?

Obsidian suits people who want local Markdown files, backlinks and plugins; Notion suits people who like databases and structured views. Both are strong for synthesis; neither handles paper capture or review on its own.

What is progressive summarization?

A method popularized by Tiago Forte in which you distill notes in layers—bolding the key passages, highlighting the best of those, then summarizing—so each note gets quicker to use every time you revisit it.

Do I need to move every note into my vault?

No, and that is the point. Move only the ideas that have come back in review and still matter. Everything else stays filed by book and chapter in the reading app.

Does this work for fiction?

Yes, with a lighter touch. Capture lines, characters and themes as you read; daily resurfacing is often enough, and only the pieces you plan to write about need the synthesis step.