Obsidian is a very feature-packed app, but it can get messy if you’re not careful when setting up your first vault. This can happen when you read about its best features and rush the setup, so you end up with a huge set of notes to try Graph View. Without a few simple habits, you may waste valuable time cleaning things up later.

I thought Graph View looked great, and I rushed to create my vault to see how all my ideas connected. But I soon found myself spending longer to find keynotes because I’d filled my vault with throwaway files. I wish someone had given me a quick heads-up before I created my first vault. So, you don’t have to repeat my mistakes. Here are three quick tips to save you time and frustration when setting up your vault.

End every session with a 5-minute cleanup

Delete throwaway notes before they pile up

When you take a lot of notes, it’s easy to create temporary ones that you only need today. If you don’t set aside five minutes to clean up at the end of your session, those temporary notes become clutter. You’ll also waste time hunting for a specific note, especially when your folders or notes have similar titles.

If deleting files or folders makes you nervous, move them to a "Review later" folder and review them when you’re not in a hurry. But if you see notes you haven’t used in at least two weeks, consider deleting them.

When I created my first vault, I rushed to make as many notes as possible. I didn’t make time to clear temporary notes from my vault until I saw how long I spent searching. Then I had to clean up my vault. I wasn’t happy about it, but I knew it would pay off in the end.

Use 4 or 5-pillar folders only

Start with the basics, such as Work, Personal, Learning, and Admin

It’s tempting to create a folder for every idea that crosses your mind. Start with a few pillars and stop there. Four or five is enough: Personal projects, Work, Pet Care, and so on. Following this pattern helps keep your notes relevant and provides a clearer view of how your notes are connected. Once you have created all the basic but important files, you can continue by adding the necessary notes for every folder.

I made the mistake of creating so many folders that, when I later cleaned up most of them, I could only wonder what I’d been thinking. I ended up spending time on cleanup instead of doing something more productive. Creating too many folders only cluttered the sidebar and slowed down my workflow. Since switching to only having pillars, I spend less time hunting and more time writing because search, backlinks, and tags surface what I need without having to wade through a long list of folders.

Don’t leave notes unlinked

Backlinks surface related notes right when you need them

Linking your notes from the very beginning is important because it can give you a new understanding of them. When you see how your notes are connected, you come up with new ideas you may not have thought of with a single page. Linking them also helps you save time by eliminating the need to retype the same information multiple times. Simply link to that page and keep it concise. Resist linking for a tiny, throwaway mention. If the connection is trivial, skip it and reserve links for pages you’ll actually revisit.

While working on a project, I remembered I had a note with various hotkeys. Instead of typing the shortcuts all over again on another note, I simply linked that note so I could refer to it later if needed. Also, you create the link to another note. Obsidian adds the backlink automatically. When you link a note to another, the target automatically displays a backlink to the source. That makes it easy to return to the original.

Small habits that keep your vault light

Obsidian works best when you keep the setup simple and build habits. One of the best ways to start is to use four or five-pillar folders, so new notes have a clear home. End each session with a five-minute cleanup to delete throwaway notes, correct names, and link the most important notes. Don’t forget to use links from the very beginning to surface related work when you return. That way, your vault stays clean, and you get things done faster.

It’s important to develop these habits to get the most out of Obsidian and enjoy using it instead of feeling lost in the sea of notes you’ll eventually have. It may require some time to get used to these habits, but they’ll pay off in the future.