Setting up Notion and Obsidian from scratch
Alright, so picture this: you’ve just decided to build a real knowledge base, not just a dump of random notes. Something you can actually trust. I tried doing that with both Notion and Obsidian at the same time (which, yes, was chaotic). But here’s how things shook out when setting each up from zero.
In Notion, setup happens in a browser tab where you’ll lose your place 5 times because the left sidebar decides to collapse every 3 seconds. It starts smooth—create a workspace, name it something ambitious like “Knowledge Vault,” and boom, you’re inside. But unless you’ve used Notion-style databases before, the interface will feel like a blank IKEA instruction manual. You can type anywhere, transform any block into anything else (e.g. a bullet becomes a toggle becomes a page inside a page). Powerful? Yes. But predictable? Lol, nope.
Creating your first knowledge base structure on Notion usually goes like:
– Page called “Resources”
– Sub-pages like “Workflows,” “Snippets,” “Project Notes”
– Accidentally create a database when you meant to make a toggle list
Obsidian feels more like waking up inside a cabin where you have to build your own furniture. You download it, create a vault on your computer (literally a folder on your hard drive), and then you’re staring at a dark, Markdown-only window that dares you to figure it out. And I mean that in a good way 🙂
Structure in Obsidian is entirely up to you. I started with three folders:
– 00 Inbox
– 01 Notes
– 02 References
Then I slapped an index.md file into the root directory. That was my manual homepage. I had to build all navigation myself — no sidebar tricks, no built-in nav buttons. Which is weirdly satisfying if you like control.
Linking information across pages
This is where things started getting interesting.
In Notion, linking between pages is fancy and visual. You can type [[ and it offers a dropdown of matching pages. Click one, and it creates a tidy inline link. Also, because Notion runs on blocks, you can reference and sync entire blocks across pages—handy if you want the same definition or checklist visible in more than one place. The kicker? Those block references often get silently unlinked if you delete/reorder content and forget—not a bug, just a devilish behavior.
Obsidian, meanwhile, eats links for breakfast. Linking a page is just [[Page Name]] in Markdown. Want to see all the backlinks pointing to a page? That’s built-in. Want to make a graph of them? Also built-in. I once created a whole structure where I didn’t even use folders—just pages linked to each other hierarchically. That would be a literal disaster in Notion 🙂
But there’s a weird catch. In Obsidian, links can silently break if you rename a file outside Obsidian (say, in your file explorer). By default, it won’t update the backlinks unless you toggle the “Automatically update internal links” setting in Preferences → Files & Links. And yes, mine randomly reset during an update once. It wrecked a week’s worth of structured content. That’s why I always peek at that setting now when something looks suspiciously disconnected ¯\_(ツ)_/¯
Syncing and access across devices
This is the part that killed me.
In theory, both tools let you access your knowledge base everywhere.
Notion just… works. No syncing setup. You log in anywhere (browser or mobile app) and your data is there. But mobile Notion is its own kind of pain. You tap a link, it opens a new page, the keyboard covers half the screen, and God forbid you try to use slash commands—weird stuff will happen.
Obsidian makes you work for sync. The app itself is free, but syncing isn’t—unless you rig your own setup. I used Dropbox first, which was smooth until one day it just stopped syncing on my phone. Turned out Obsidian Mobile doesn’t respect some of Dropbox’s cache timing. Then I tried Git syncing through a plugin, which worked but required me to set up SSH keys and remember terminal commands. (I definitely did not.)
Eventually, I paid for Obsidian Sync. It solved the problem, but added subtle lag when switching notes if you kept the vault open in two devices at once. Nothing breaks, but edits can get “merged” in weird ways unless you close and reopen.
Adding tags and metadata to notes
This one tripped me up more than I expected.
In Notion, you probably assume you can tag things with hashtags. Nope. Tags in Notion are best done as databases with select or multi-select fields. So you end up creating a table view, adding a “Tags” column, and assigning them that way. Visual? Yes. Fast? Not really. You also can’t bulk-edit these fields easily without selecting rows manually.
In Obsidian, tags are just #hashtagged directly in your notes.🔥 You can type #projectX anywhere and see it pop up in the tag pane. Obsidian doesn’t care where the tag lives in the note, and as long as it’s consistent, you can sort by it later.
But metadata gets gnarly. Formal frontmatter metadata (like title, created, tags) lives in YAML format at the top of the note. Something like:
“`yaml
title: Meeting Notes
tags: [client, Q2]
“`
If you’ve never seen YAML before, it looks like a grocery list for tech robots. Also, not all community plugins respect it. So if you tag your notes this way and your search plugin ignores frontmatter (some do), you’re gonna think your data is disappearing.
Notion doesn’t use any of this. Everything’s visible and editable like a spreadsheet. Obsidian feels like doing brain surgery with gloves off.
Collaboration and team sharing
Okay, let’s just say this one’s Notion’s game to lose.
Notion lets you invite collaborators, assign tasks, mention people, and show person columns—all built-in. Sharing a page with someone is literally a toggle. I’ve had teammates update my tables in real time while we were both in Zoom. It’s seamless, almost too seamless. The one thing I will say: editing permission bugs do happen. I once accidentally let an intern edit our master template because the sharing settings silently inherited from a parent page 🙁
In Obsidian, real-time collaboration is basically not a thing. There’s no native support for multiple users editing at once. Yes, you can share a vault through Git or sync it via a common folder service (like Dropbox or GitHub), but if two people edit the same note at once? Good luck. Last-write wins. You’ll probably overwrite each other unless you manually pause and check first.
Honestly, I only use Obsidian for pure solo work now. It’s just not built for teams unless the team enjoys Git conflict resolution as a bonding activity. 😛
Using plugins and automating workflows
This was the fun part… followed by breakage.
Obsidian has a plugin ecosystem that’s borderline magical. You go into Settings → Community Plugins, enable Safe Mode off (scary but fine), and then you can install from hundreds of tools. I’m using Dataview, Calendar, QuickAdd, and Templater—which together basically turned my notes into a living database. Dataview lets you write queries like “show me all notes tagged #meeting created this month.” Insanely powerful.
But also, each plugin can break with zero warning after an update. My Calendar stopped loading for a whole day because I had a conflicting CSS snippet enabled. You won’t get a nice error—stuff just silently vanishes. When things go sideways, I usually toggle plugins off one by one, relaunch, and yell at my screen a little. Obsidian forums help, but it feels very do-it-yourself.
Notion does support automation, but not the same way. You can integrate it with Zapier or Make to trigger things like “add new row in Notion database when a new email comes in.” That’s fine, but the syntax is always more clunky than it needs to be—every Notion field is a long dropdown with weird field names like properties.title.rich_text. I spent an hour debugging automation that broke because the Notion database name had an emoji in it. Yep.
Searching and retrieving information later
This is honestly the most important part of any knowledge base, and both tools do it wildly differently.
In Notion, search is friendly—type a word, get a dropdown of results with visible snippets. But it doesn’t show you *where* in the structure your results live unless you manually open each one. Also, if you name multiple subpages “Meeting Notes” (which I have), all the results look the same. Add in the fact that search indexing has a little lag, and you’ll sometimes find yourself typing a title you just added… and getting nothing back.
Obsidian search is raw but precise. Hit Cmd+Shift+F and boom—text-level search across every file. Supports regex (if you’re into that), filters like path: or tag:, and shows exact lines in context. I once ran a live client call with my Obsidian search pane open just to track down policy snippets. It’s that fast.
But if your notes aren’t well-structured or you forgot how you tagged something, Obsidian won’t save you with fuzzy logic. It’s more like grep than Google. And the sidebar gets cluttered fast if you don’t manage your folder layout carefully.
Which tool I actually keep using
Here’s the messy truth: I actually use both. But not for the same things.
Notion holds all shared stuff—project dashboards, client deliverables, shared templates. Basically anything where someone else has to look at it.
Obsidian holds my brain. Meeting notes, research, code snippets, article drafts. Stuff that I don’t want structured until I’ve figured it out. If it touches Markdown and I need it to last, it goes into the vault.
I used to try and make The One Perfect System, but all that did was create a beautiful graveyard of half-filled dashboards ☹