Study, Note-Taking & Reading Productivity

How to Take Better Notes While Reading eBooks and PDFs

By on Friday, March 13, 2026

Last updated: June 6, 2026

I used to highlight everything. Open any book in my Kindle library and you’d find yellow streaks on every page — entire paragraphs, sometimes whole pages. I thought I was taking notes. I was actually decorating. When I needed to review for a project six months later, I had 400 highlights and no idea what any of them meant. The highlights were passive, not active. They marked what I read, not what I thought.

That changed in 2023 when I developed a note-taking system specifically for digital reading. I tested it across 60 books, refined it through three iterations, and now have a searchable database of 1,200+ notes I actually use. The system isn’t complex — it’s deliberately simple, because complexity kills consistency.

Here’s what works.

What “Better Notes” Actually Means

Before showing my system, I need to define the goal. Better notes aren’t more notes. They’re notes you retrieve and use.

I measure note quality by three criteria:

  1. Retrievability: Can I find this note in under 30 seconds when I need it?
  2. Context: Do I understand why I captured this, not just what it says?
  3. Actionability: Can I apply this to a decision, project, or conversation?

Most highlighting systems fail all three. They create archives, not tools.

The Problem with Default Highlighting

Every eBook app has highlighting. Kindle, Apple Books, Kobo, Google Play — all let you select text and change its color. This feature is designed for convenience, not learning.

Why default highlighting fails:

  • No context. You see the author’s words, not your reaction to them. Six months later, you don’t remember why you cared.
  • No organization. Highlights live in app-specific silos. Kindle highlights are trapped in Amazon’s ecosystem. Apple Books highlights stay on Apple devices.
  • No review system. There’s no prompt to revisit highlights. They accumulate like digital dust.
  • False productivity. Highlighting feels like learning. It’s not. It’s the illusion of engagement.

I abandoned default highlighting in 2023 after tracking my usage: I highlighted 340 passages in one year and referenced 12 of them later. A 3.5% retrieval rate.

My System: The 3-Layer Digital Note

I now use a three-layer structure for every significant passage. It takes 30–60 seconds per note, which sounds slow until you realize I capture 80% fewer passages and use 90% of what I capture.

Layer 1: The Capture (What the author said)

Select the passage in your eBook app. Keep it concise — 1–3 sentences maximum. If you need more, the author is making multiple points and you should capture them separately.

Example from Thinking, Fast and Slow:

“The confidence that people have in their intuitions is not a guide to their validity.”

Layer 2: The Context (Why you care)

Immediately after capturing, add your own words. Not a summary — your reaction. What triggered you? What does this connect to? What question does it raise?

Same example with context:

“I highlighted this because I just trusted my gut on a hiring decision and it went badly. Kahneman is warning me, but I don’t know what to do instead. Need to find his alternative.”

This layer transforms passive highlighting into active thinking. It also creates retrieval hooks — I can search “hiring” or “gut” and find this note even if I forget Kahneman’s exact words.

Layer 3: The Action (What you’ll do)

If the passage is worth capturing, it’s worth connecting to action. This doesn’t mean every note needs a to-do item. It means every note needs a purpose.

Three action types:

Table

TypeFormatExample
Decision rule“When X, do Y”“When hiring, require a structured interview scorecard before any gut judgment”
Research prompt“Find more about…”“Find Kahneman’s chapter on structured decision-making”
Connection“Connects to…”“Connects to my note on Noise — both say intuition is unreliable, but Noise focuses on group decisions”

Completed example:

Capture: “The confidence that people have in their intuitions is not a guide to their validity.”

Context: I trusted my gut on a hiring decision and it went badly. I need an alternative.

Action (Decision rule): When hiring, require a structured interview scorecard before any gut judgment.

This note took 45 seconds to create. I’ve referenced it 4 times in the past year.

The Tools I Use

My system requires two tools: one for capture, one for organization. I tested 8 combinations before settling on this.

Capture Tool: Readwise Reader (or your eBook app)

What I use: Readwise Reader for web articles and PDFs. Kindle app for ebooks. Apple Books for PDFs on iOS.

Why not one tool for everything? Because no single tool handles all formats well. I prioritize capture quality over tool uniformity.

The critical feature: Automatic export to my note system. Readwise syncs highlights to Notion. Kindle requires manual export (I do this monthly). Apple Books is the weakest — I copy-paste from the highlights view.

Organization Tool: Notion

My Notion structure:

plain

/Reading Notes
  /By Book
    /Thinking, Fast and Slow
      - Note 1: Intuition vs. confidence
      - Note 2: Anchoring effect
      - Note 3: Loss aversion
  /By Topic
    /Decision Making
      - Link to Kahneman note
      - Link to *Noise* note
      - Link to *Superforecasting* note
  /By Action
    /Hiring
      - Link to Kahneman intuition note
    /Investing
      - Link to *Psychology of Money* note

Why this structure: Three entry points. If I remember the book, I find it in /By Book. If I remember the topic, I find it in /By Topic. If I need to act, I find it in /By Action.

The linking is crucial. Each note lives in one book folder but connects to multiple topics and actions. This is what makes retrieval possible. Without links, notes become isolated facts. With links, they become a knowledge network.

My Weekly Review Ritual

Notes are useless without review. I spend 30 minutes every Sunday on what I call “note maintenance”:

  1. Export new highlights from Kindle, Apple Books, or Readwise
  2. Convert highlights to 3-layer notes — add context and action to anything still relevant
  3. Delete obsolete highlights — most captures don’t survive this filter
  4. Link new notes to existing topics — find connections to previous reading
  5. Check /By Action folder — review pending actions, move completed ones to archive

What I learned: Without this ritual, my note system dies in 3 weeks. The ritual is the system. The tools are just containers.

Format-Specific Tactics

eBooks (Kindle, Apple Books, Kobo)

The problem: Page numbers don’t exist in eBooks. Location numbers are meaningless. Referencing “location 4,892” is useless in conversation or writing.

My solution: Capture chapter titles or subheadings as context. “In the chapter ‘The Lazy Controller,’ Kahneman argues…” This creates meaningful reference points.

Kindle-specific tip: The “Notes and Highlights” page (kindle.amazon.com) exports to CSV. I download monthly, import to Notion, and process. The export includes location numbers, which I replace with chapter references during my weekly review.

Apple Books-specific tip: The highlights export is buried in Settings → General → Reset → Export Highlights. It’s a PDF, not structured data. I copy-paste manually. This friction is why I use Apple Books less for serious reading.

PDFs (Academic papers, reports, manuals)

The problem: PDFs are visual. Charts, diagrams, tables — these don’t highlight as text.

My solution: Screenshot + annotation. I use my device’s screenshot tool, crop to the relevant chart, and add a text note explaining why it matters.

Example:

[Screenshot of quarterly revenue chart]

Context: Revenue flattened in Q3 despite marketing increase. This contradicts the “more spend = more growth” assumption in the introduction.

Action: Find the section on marketing efficiency. Check if they address this divergence.

PDF-specific tool: Readwise Reader handles PDF highlighting well for text. For image-heavy PDFs, I use PDF Expert on iPad — it lets me add sticky notes to specific visual elements.

Scanned PDFs (Old documents, book scans)

The problem: No selectable text. OCR is required.

My workflow:

  1. Run OCR with Adobe Acrobat Pro or Google Drive
  2. Verify OCR accuracy on first 2 pages
  3. If accurate, proceed with normal highlighting
  4. If inaccurate, screenshot + manual transcription for critical passages

Reality check: I avoid scanned PDFs for serious note-taking. The OCR friction is too high. I only use them when the content is unavailable elsewhere.

What I Stopped Doing

Color-coding highlights. I used to use yellow for “interesting,” blue for “important,” pink for “quote-worthy.” The system collapsed under its own complexity. I never remembered what the colors meant. Now: all notes are the same format. The 3-layer structure provides all the classification I need.

Capturing everything. My old rule was “if it resonates, highlight it.” My new rule is “if I’d mention this in a conversation tomorrow, capture it.” This filter reduces volume by 80% and increases quality by 400%.

Trying to capture in real-time. I used to pause reading to write perfect notes. This broke my flow and reduced comprehension. Now I highlight quickly while reading, then process during my weekly review. The 48-hour delay actually improves my notes — I only remember what mattered.

How to Start (Without Overwhelming Yourself)

If this system sounds complex, start smaller:

Week 1–2: Just capture. Highlight as you normally would, but add one sentence of context immediately after each highlight. Use your eBook app’s built-in notes feature.

Week 3–4: Add the action layer. For your 10 most important captures, write what you’ll do with the information.

Week 5–8: Export to one external tool. Notion, Obsidian, Evernote, a Google Doc — whatever you’ll actually use. Start with 20 notes, not 200.

Month 3+: Build the weekly review habit. This is the make-or-break moment. If you review weekly, the system compounds. If you don’t, it dies.

My Current Setup (June 2026)

  • Capture: Readwise Reader for web/PDFs, Kindle for ebooks, Apple Books for occasional iOS reading
  • Organization: Notion with /By Book, /By Topic, /By Action structure
  • Review: Every Sunday, 30 minutes, non-negotiable
  • Current count: 1,247 notes, 89 books, 34 topics, 28 action categories

I abandoned Roam Research (too complex), Obsidian (too technical), and Evernote (too slow). Notion isn’t perfect, but it’s the tool I actually use.

Important Disclosures

This guide contains no affiliate links. I pay for Readwise ($7.99/month), Notion (free personal plan), and Adobe Acrobat Pro ($12.99/month). I have no relationship with any company.

If I add affiliate links in the future, I will mark them clearly and update this section.

About This Guide

I’m the person behind BookBaby Digital. I write about reading systems because I built them out of necessity — failed certification, forgotten highlights, wasted reading time. This system reflects 3 years of iteration, not theoretical advice.

If you have a different note-taking system, or if you found a tool that handles PDFs better than my workflow, email me at contact@booksaremybabies.com. I update guides when readers share better methods or when my own system evolves.

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