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Why obsidian wins the second brain war and notion just can’t keep up

the markdown-powered beast that turned my cluttered mind into a structured wiki with backlinks and magic Section 1: introduction the brain fog problem Let’s be real for a sec most of us are drowning in digital clutter. You open Notion to “organize” your notes and suddenly spend 45 minutes tweaking page aesthetics like you’re designing a landing page for a failed SaaS. You try Craft and get distracted by the beautiful UI because it’s basically Apple Notes with a Gatsby filter. Capacities? Promising, but slow. And you still can’t remember where you wrote that idea about “building an indie dev SaaS for LLM-powered cats.” We’re knowledge workers in the age of information overload, and ironically, all our shiny productivity tools are making us feel… less productive. Here’s the core problem: these apps want to organize your thinking for you. But what if you could build a system that works with your brain, not against it? That’s where Obsidian stepped in for me. No fluff. No clunky databases. No “Sorry, this page is still loading.” Just plain text, local files, and the power to shape my knowledge the way I think like a dev. Or a gamer grinding XP in a skill tree of ideas. This isn’t just another productivity tool. Obsidian is a thinking environment. And once you get used to it, going back to block-based apps feels like trying to write code in Google Slides. TL;DR: Notion is the IKEA of note-taking pre-built furniture for your ideas. Obsidian is Minecraft. Build your Second Brain from raw markdown blocks. Section 2: the difference isn’t shiny it’s structural Let’s cut through the hype. When you open Notion, it feels like a Silicon Valley co-working space. Sleek. Minimalist. Buzzing with “startup energy.” You’re greeted by templates, icons, widgets, and the false hope that this time, your life will actually get organized. Craft? Even prettier. It feels like journaling in an art gallery until you try to scale up or connect ideas and realize it’s all surface, no depth. Capacities? Conceptually cool. But performance is sluggish, and the UX assumes you want your thoughts to live in someone else’s taxonomy. Now open Obsidian. You’re staring at a blank markdown file. No clutter. No artificial structure. Just you and your brain. It’s… intimidating. But also freeing. Like Vim for your mind. Here’s the fundamental difference: Obsidian is structural. It doesn’t just help you store knowledge it helps you shape it. While most apps think in pages and databases, Obsidian thinks in connections. Notes link, loop, and evolve like neurons in a living brain. That’s why it clicks with developers, writers, researchers anyone who needs more than a static to-do list. It’s not here to be pretty. It’s here to be useful. “The best tools don’t get in your way. They get out of it.”probably some dev who mapped their whole life in a markdown vault Want to see how markdown beats blocks to the punch? Section 3: markdown > block-based thinking Let’s talk markdown the raw, nerdy, glorious markup language that fuels Obsidian. While Notion fans are still fiddling with /commands, column widths, and toggles nested inside toggles like some Russian doll of productivity, Obsidian users are just… writing. Because markdown is fast. It’s lean. It’s plain text. It’s what devs already use in README files, changelogs, blogs, and wikis. It’s the language of the web, the command line, and now your brain. Want a heading? ## Bullet point? - Link to another note? [[note title]] Code block? No clicking. No dragging. No hunting for UI elements buried three toolbars deep. You get out of your own way and into the zone keyboard only, baby.Meanwhile, block-based apps like Notion force you into their way of thinking. Everything’s a block. Want to move a sentence? Grab the handle. Want to style something? Click, click, click.It’s like trying to write a novel in PowerPoint.Markdown, on the other hand, makes your thoughts portable. The note you wrote in Obsidian can be opened in VS Code, shared via GitHub, or published directly to your blog. No export drama. No vendor lock-in.You don’t “fight” markdown. You ride it like a wave.And that’s the core of it: Speed Simplicity Power No distractions. No bloat. Just writing, linking, thinking.If you’ve ever tried to write technical docs, journal ideas, or sketch an app feature roadmap, you know the pain of formatting taking over your flow.With Obsidian, your keyboard is your superpower. Everything else? Plugins, if you want them. But not required.TL;DR: Markdown is the git of note-taking minimal, versionable, and developer-native.Section 4: your notes are files, not prisonersLet’s get this out of the way: Notion, Capacities, and Craft all have beautiful interfaces but your notes? They live in a walled garden.Try exporting a full workspace from Notion and you’ll end up with a zip file full of chaos. Try moving data from Capacities into anything else and it’s like unzipping Schrödinger’s folder you don’t know what state your notes a

May 9, 2025 - 09:26
 0
Why obsidian wins the second brain war and notion just can’t keep up

the markdown-powered beast that turned my cluttered mind into a structured wiki with backlinks and magic

Section 1: introduction the brain fog problem

Let’s be real for a sec most of us are drowning in digital clutter.

You open Notion to “organize” your notes and suddenly spend 45 minutes tweaking page aesthetics like you’re designing a landing page for a failed SaaS. You try Craft and get distracted by the beautiful UI because it’s basically Apple Notes with a Gatsby filter. Capacities? Promising, but slow. And you still can’t remember where you wrote that idea about “building an indie dev SaaS for LLM-powered cats.”

We’re knowledge workers in the age of information overload, and ironically, all our shiny productivity tools are making us feel… less productive.

Here’s the core problem: these apps want to organize your thinking for you.
But what if you could build a system that works with your brain, not against it?

That’s where Obsidian stepped in for me. No fluff. No clunky databases. No “Sorry, this page is still loading.” Just plain text, local files, and the power to shape my knowledge the way I think like a dev. Or a gamer grinding XP in a skill tree of ideas.

This isn’t just another productivity tool. Obsidian is a thinking environment.
And once you get used to it, going back to block-based apps feels like trying to write code in Google Slides.

TL;DR: Notion is the IKEA of note-taking pre-built furniture for your ideas. Obsidian is Minecraft. Build your Second Brain from raw markdown blocks.

Section 2: the difference isn’t shiny it’s structural

Let’s cut through the hype.

When you open Notion, it feels like a Silicon Valley co-working space. Sleek. Minimalist. Buzzing with “startup energy.” You’re greeted by templates, icons, widgets, and the false hope that this time, your life will actually get organized.

Craft? Even prettier. It feels like journaling in an art gallery until you try to scale up or connect ideas and realize it’s all surface, no depth.

Capacities? Conceptually cool. But performance is sluggish, and the UX assumes you want your thoughts to live in someone else’s taxonomy.

Now open Obsidian.

You’re staring at a blank markdown file. No clutter. No artificial structure. Just you and your brain.
It’s… intimidating. But also freeing. Like Vim for your mind.

Here’s the fundamental difference:

Obsidian is structural. It doesn’t just help you store knowledge it helps you shape it.

While most apps think in pages and databases, Obsidian thinks in connections. Notes link, loop, and evolve like neurons in a living brain.

That’s why it clicks with developers, writers, researchers anyone who needs more than a static to-do list. It’s not here to be pretty. It’s here to be useful.

“The best tools don’t get in your way. They get out of it.”
probably some dev who mapped their whole life in a markdown vault

Want to see how markdown beats blocks to the punch?

Section 3: markdown > block-based thinking

Let’s talk markdown the raw, nerdy, glorious markup language that fuels Obsidian.

While Notion fans are still fiddling with /commands, column widths, and toggles nested inside toggles like some Russian doll of productivity, Obsidian users are just… writing.

Because markdown is fast.
It’s lean. It’s plain text. It’s what devs already use in README files, changelogs, blogs, and wikis. It’s the language of the web, the command line, and now your brain.

Want a heading? ##
Bullet point? -
Link to another note? [[note title]]
Code block?

No clicking. No dragging. No hunting for UI elements buried three toolbars deep.
You get out of your own way and into the zone keyboard only, baby.

Meanwhile, block-based apps like Notion force you into their way of thinking.
Everything’s a block. Want to move a sentence? Grab the handle. Want to style something? Click, click, click.

It’s like trying to write a novel in PowerPoint.

Markdown, on the other hand, makes your thoughts portable. The note you wrote in Obsidian can be opened in VS Code, shared via GitHub, or published directly to your blog. No export drama. No vendor lock-in.

You don’t “fight” markdown. You ride it like a wave.

And that’s the core of it:

  • Speed
  • Simplicity
  • Power

No distractions. No bloat. Just writing, linking, thinking.

If you’ve ever tried to write technical docs, journal ideas, or sketch an app feature roadmap, you know the pain of formatting taking over your flow.

With Obsidian, your keyboard is your superpower.
Everything else? Plugins, if you want them. But not required.

TL;DR: Markdown is the git of note-taking minimal, versionable, and developer-native.

Section 4: your notes are files, not prisoners

Let’s get this out of the way:
Notion, Capacities, and Craft all have beautiful interfaces but your notes?
They live in a walled garden.

Try exporting a full workspace from Notion and you’ll end up with a zip file full of chaos. Try moving data from Capacities into anything else and it’s like unzipping Schrödinger’s folder you don’t know what state your notes are in until you break them open, and by then, they’re half-broken.

Obsidian doesn’t play that game.

Every single note is a plain .md file living in a folder on your machine. It’s yours. Forever.
No internet? Doesn’t matter.
Want to back it up? Git it. Literally.
Need to move it? Just drag the folder somewhere else.

This is the part that power users and developers really get excited about. Because it means:

  • Your Second Brain works offline by default
  • You can sync it however you want: Dropbox, GitHub, iCloud, Syncthing, etc.
  • You can version control it, diff it, grep it anything you’d do with code
  • You’re not locked into a platform that might change its pricing next Tuesday

It’s the UNIX philosophy of note-taking:

  • Do one thing well
  • Let the user decide how to extend it
  • Keep it modular, portable, and transparent

And in a world where platforms rise and fall faster than crypto tokens, owning your data isn’t a “nice to have” it’s survival.

Imagine writing 10 years of thoughts in Notion, only to lose it all to a billing issue or a broken export.
With Obsidian, your vault lives where you live: on your disk.

Bonus: Want to sync between laptop and phone? Use Obsidian Sync, or roll your own with iCloud, Git, or even a cron job. You’re in control.

Up next: the fun stuff.

Section 5: plugins are where obsidian becomes an RPG

Here’s where Obsidian really pulls out the +10 Sword of Customization and cleaves through the cookie-cutter crowd.

Out of the box, Obsidian is clean and minimal. But once you open the Community Plugins tab, it’s like stepping into Skyrim with mod support.

Over 1,000 plugins, all built by nerds like us who thought,

“Hmm, what if my note-taking app could also be a task manager, a spaced repetition system, a database, and a blog engine?”

And so it is.

A few plugin bangers worth leveling up for:

  • Templater Add dynamic templates using JavaScript. Yes, actual logic in your notes.
  • Dataview Turn your markdown notes into interactive dashboards. Query your notes like they’re a database:
    table file.mtime from "Books" where rating >= 4
  • Advanced Tables Markdown tables without losing your sanity.
  • Calendar + Daily Notes Auto-create dated notes, journal-style.
  • Canvas Visual canvas for non-linear thinking. Draw connections like a detective with red string.

And yes, there are GPT-based tools too. Like Smart Connections that help you auto-link notes, or writing assistants to flesh out your thoughts.

It’s like building your own Second Brain…
But instead of buying features from a SaaS product manager’s backlog, you’re crafting your own toolkit one plugin at a time.

Devs love this stuff because:

  • You can hack Obsidian with TypeScript plugins
  • You can automate workflows (note refactoring, project tracking, etc.)
  • You can run custom JS on open because why not?

Obsidian is less like Evernote, more like Emacs with a dark theme.

It’s the Minecraft of productivity tools simple blocks, infinite complexity.

And when your note-taking app starts feeling like a game…
That’s when you know it’s good.

Next: we hit the dopamine machine of connected thought

Section 6: backlinking and graph view: the dopamine loop

Here’s where Obsidian flexes its brain-like behavior and completely changes how you think about thinking.

Let’s talk backlinks.

In most apps, a note is a lonely island. You write it, you close it, and eventually forget it exists. But in Obsidian, the second you write [[That Other Note]], a bidirectional link is formed.

Now both notes know they’re connected. You don’t have to manually keep track the system does it for you.

It’s like tagging someone on social media. The link isn’t just blue — it’s alive.

Why this is huge:

  • You start writing without worrying about structure because connections come later.
  • Old ideas resurface naturally, just by linking in new notes.
  • You discover relationships between topics you didn’t know existed.

Imagine writing a note on “JavaScript Closures” and later writing another about “Memory Management.” Link one to the other and boom you’ve created a conceptual bridge. And over time? Your vault becomes a knowledge web, not just a folder full of orphaned markdown files.

Enter: The Graph View

Now this is the part that’ll trigger the “ooh shiny!” reflex in your dev brain.

The Graph View visualizes your notes as nodes and links like a mind map on steroids.
You can filter it, group by tags or folders, adjust physics, and even watch your ideas grow like a neural net.

Is it useful?

Yes.
Is it also 100% dopamine bait?
Also yes.

It gives you a bird’s-eye view of how your thoughts connect, and that insight alone makes you want to write more, link more, and explore your own ideas.

Notion: “Here’s a page.”
 Obsidian: “Here’s a galaxy.”

This is where second brain systems like Zettelkasten and PARA come to life not as frameworks, but as emergent behaviors from linking your ideas.

And yes, it feels like hacking your own brain.

Section 7: how I use obsidian like a dev

Alright, time to pop the hood.

This section is for the builder brains the devs, the sysadmins, the techie tinkerers who don’t want a pretty journal. They want a command center. That’s exactly what Obsidian becomes when you dial it in right.

Here’s how I’ve wired up my Second Brain like a dev:

Daily notes for logs and commits

Every day starts with a fresh daily note, auto-generated using the Templater plugin. It includes:

  • A checklist for my morning routine
  • A code review log
  • Scratchpad for bug notes and design ideas
  • Timestamped “commits” like:
    11:20 AM - Fixed the failing auth test (JWT mismatch)

Feels like journaling, but also like git log for my brain.

Folder structure like a repo

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