How to Build a Linked Notes Vault With Obsidian, Step by Step

I had three years of notes scattered across five apps before I actually sat down and asked myself a simple question: when I need something I wrote eight months ago, do I ever actually find it? The honest answer was no. I'd remember writing it and then spend twenty minutes searching four apps that weren't the right one. Obsidian is the one place I've built where a note from March genuinely resurfaces when I'm writing something related in August, because the notes point at each other instead of sitting in separate, sealed folders.

This is beginner level: no code, no paid plan required, and the whole setup below took me under an hour the first time. If you already run a structured system in Notion and just want to know whether this is worth switching to, my Notion second brain guide is the closer comparison — read to the end here first, because the two solve genuinely different problems rather than the same one twice.

The problem: notes that never talk to each other

Most note apps are filing cabinets. You write something, you pick a folder, and the note sits there until you remember which folder you put it in. That works fine for notes you'll only ever look up by name — a recipe, a password reset code. It falls apart for the notes that actually matter to how you think, because those notes are rarely about one thing. A note on a client project touches a note about a tool I use, which touches a note about a mistake I made on a completely different project eighteen months earlier. A folder can only hold a note in one place. A link can hold it in as many places as it's actually relevant.

The moment this clicked for me was rereading an old project note and realising I'd solved the exact same problem twice, eleven months apart, because nothing connected the two notes and I had no way of finding the first one short of remembering it existed. That's the gap a linked vault closes.

What Obsidian actually is

Obsidian is a note-taking app that stores every note as a plain text file on your own computer, and lets you link any note to any other note by typing its title inside double square brackets. Type [[Client onboarding]] inside any note and it becomes a clickable link to a note called "Client onboarding" — creating it automatically if it doesn't exist yet. Every link is two-way: open "Client onboarding" and you'll see a "Linked mentions" panel at the bottom listing every note that links to it, even ones you wrote months apart and never consciously connected. That backlink panel is the entire trick. You don't have to remember where you filed something; you follow the links from wherever you already are.

The graph view takes that a step further, drawing every note in your vault as a dot and every link as a line between them — so clusters of genuinely related thinking become visible as clusters, not as a list you have to read top to bottom. It's a nice-to-have rather than the point, but it's the fastest way to spot a topic you've written about more than you realised.

Step 1: Install Obsidian and create your vault

Download Obsidian free from obsidian.md for Mac, Windows, Linux, iOS or Android, and on first launch choose "Create new vault." A vault is just a folder — Obsidian will create one wherever you point it, and every note you write from here on is a plain .md text file sitting inside it. I keep mine in a folder synced through iCloud Drive so it's identical on my laptop and phone without paying for Obsidian's own sync service, though that official Sync option exists if you'd rather not rely on a third-party sync tool. Name the vault something you won't want to rename in six months — mine is just "Notes."

Step 2: Set a light folder structure — then mostly ignore it

Create three or four top-level folders that match the broad areas of your life or work: I run "Business," "Projects," "Reading" and "Journal." That's it. The instinct coming from a filing-cabinet app is to build twenty nested subfolders before writing a single note — resist it. The whole point of this system is that links do the organising work folders used to do, so an over-built folder tree just adds friction without adding any real structure. If a note doesn't obviously belong in one of your four folders, it probably belongs in all of them a little, which is exactly what a link is for.

Step 3: Write your first notes and link them as you go

Start writing normally, and the moment you mention something that could be its own note — a person, a project, a concept you'll want to find again — wrap it in double square brackets. Writing a note about a client call — even the three lines I take by hand over an AI transcript — and you mention the project it relates to? Type [[Q3 website rebuild]] right there in the sentence. If that note doesn't exist yet, Obsidian creates it the first time you click the link, empty and waiting for whatever you write into it next. Don't go back and try to link everything retroactively on day one — link forward from today, and let old notes accumulate connections naturally as you reference them again.

Step 4: Turn on graph view and actually look at it once a week

Click the graph icon in the left sidebar to see every note and link in your vault as a web. Early on it'll look sparse and a bit sad — that's normal, and it fills in fast once linking becomes a habit rather than a chore. I check mine roughly once a week, not to admire it, but because an isolated dot with no lines to it is a note that's fallen out of the loop, and seeing it visually is how I remember to go back and connect it to something.

Step 5: Add tags for the handful of things links genuinely can't do

Links are for relationships between specific notes. Tags are for cutting across the whole vault by status or type — I use exactly three: #todo for anything with an open action, #draft for half-finished writing, and #reference for notes I want to be able to pull up as a flat list regardless of what they link to. Click any tag to see every note carrying it. Resist building more than a handful — a tag system with forty tags is just a worse folder system wearing a different hat.

Step 6 (optional): Add one or two plugins, not fifty

Obsidian's community plugin store has thousands of entries and it is genuinely tempting to install a dozen the first week. Don't. I run exactly two: Templater, which drops a consistent structure into new notes so I'm not retyping the same headings every time, and Dataview, which lets one note pull together a live list of everything tagged #todo across the whole vault. Everything else I tried in year one I eventually turned back off — each plugin is another thing that can slow the app down or break on an update, and the two-way linking that makes Obsidian worth using at all is a core feature, not a plugin.

Common mistakes worth avoiding

1. Building the folder tree before writing a single note. An elaborate structure decided in advance fights the system's actual strength, which is organising itself through links after the fact.
2. Trying to link everything retroactively. Going back through months of old notes to add links is a chore that kills the habit before it starts. Link forward from today and let the backlog fill in on its own as you revisit old notes naturally.
3. Installing every plugin in the first week. Start with none, add one only when a specific, named annoyance justifies it, and remove anything you haven't opened in a month.
4. Treating tags as a second folder system. If you're creating a new tag for every note, you've rebuilt the filing cabinet you were trying to get away from — keep the tag list short enough to remember from memory.

If structured databases with proper filters and views sound closer to what you actually need than free-form linked notes, I put Notion up against a plain spreadsheet in Notion vs Spreadsheet: Which Keeps You on Track? — the honest answer for which system wins depends entirely on whether your information was structured before you wrote it down, or only became structured afterward. It sits alongside the rest of the step-by-step setups in the full AI guides library, if this kind of build is your thing.

Questions people actually ask

Is Obsidian actually free to use?

Yes, for personal use the core app is free with no note limit and no trial period — I've used it that way for three years. The paid add-ons are Sync (Obsidian's own end-to-end encrypted cloud sync between devices) and Publish (turning a vault into a public website), and neither is required to get the setup in this guide working.

Do I need to know Markdown to use Obsidian?

No. Every note opens in a live preview that renders bold, headings and links as you type, so you never have to look at raw symbols unless you want to. The only syntax worth learning on day one is double square brackets around a note title to link it — everything else you can pick up as you go.

What happens to my notes if Obsidian shuts down or I stop paying?

Nothing, because there's nothing to lose access to. A vault is just a folder of plain .md text files sitting on your own computer — Obsidian is the window you view them through, not the format they're stored in. Delete the app entirely and every note still opens in Notepad, TextEdit, or any other text editor you own.

Can I sync my vault between my phone and laptop?

Yes, several ways. Obsidian's own paid Sync service is the simplest, but because a vault is just a folder, dropping it inside iCloud Drive, Dropbox, or Google Drive and pointing the mobile app at that same folder works too — I ran it through iCloud Drive for free for over a year before switching to official Sync for the extra reliability.

How is this different from building a second brain in Notion?

Notion is databases first — properties, filters and views that reward information you can structure in advance. Obsidian is links first — you write freely and the connections between notes surface afterward through backlinks and the graph view, which suits thinking you haven't organised yet better than thinking you already have. I use Notion for the business, admin and anything with a due date, and Obsidian for the notes I couldn't have planned a database around.