Ibrah5em

Organizing an Obsidian Vault — Lessons from Doing It Wrong

3 min read

Organizing an Obsidian Vault — Lessons from Doing It Wrong

I’ve reorganized my vault multiple times. Each time I thought I was fixing it. Each time I was just rearranging the same mess into a different shape. Here’s what I eventually learned.

The Mistakes I Kept Making

Deep nesting. At one point I had paths like IT Space/AI/Notes/DL/Neural Networks/Main/. Six levels deep. Finding anything required drilling through empty folders. The fix was brutal but simple: flatten everything to 2–3 levels max.

Multiple “Notes” folders. I had a “Notes” folder inside almost every topic folder. Notes inside Projects inside Knowledge inside… more Notes. The word “Notes” should probably never be a folder name — your entire vault is notes.

Inconsistent naming. Mix of English and Arabic, spaces and hyphens, capitalized and lowercase. Pick a convention and stick with it. I settled on Kebab-Case for folders. Doesn’t matter what you pick — consistency matters.

Scattered media. Some folders had a Media subfolder, others had images dumped alongside notes. I now use _Media/ with an underscore prefix (sorts to top) inside each major topic.

Root-level chaos. Random files sitting in the vault root because I was too lazy to file them. Exam tables next to neural network notes next to personal reflections. The root should be empty except for your top-level folders.

The Structure That Works

After too many attempts, I settled on organizing by purpose, not by topic:

Vault/
├── Knowledge/        # Stuff I'm learning
├── Projects/         # Stuff I'm building
├── Personal/         # Daily notes, reflections, plans
├── University/       # Coursework (separate because it's temporary)
├── System/           # Templates, plugins, CSS, Dataview queries
└── Archive/          # Done or abandoned

Number prefixes (00-System/, 10-Knowledge/) help with sort order if your vault is large. I use them sometimes, sometimes not — depends on the vault size.

What I Stopped Doing

Stopped organizing by subject at the top level. “AI” and “Cybersecurity” and “Linux” are not top-level concerns. They’re subfolders inside Knowledge. The top level answers “what kind of thing is this?” not “what topic is it about?”

Stopped creating folders preemptively. I used to create elaborate folder structures before having any notes to put in them. Empty folders are clutter. Create the folder when you have 3+ notes that need one.

Stopped relying on folders alone. Tags + Dataview queries do more organizing than any folder structure. A note can belong to multiple contexts through tags. It can only live in one folder.

The Reorganization Checklist

If you’re about to restructure your vault:

  1. Back up everything first. Zip the entire vault.
  2. Close Obsidian while moving files in bulk.
  3. After moving, check for broken links immediately — Obsidian flags these.
  4. Update any Dataview queries that reference folder paths.
  5. Update templates that contain hardcoded paths.
  6. Test that daily note creation still works.

The biggest lesson: don’t reorganize for the sake of it. If you can find your notes, the structure is fine. Reorganize only when you genuinely can’t find things or when the friction of the current structure slows you down. If you’re reorganizing to avoid doing actual work, that’s a different problem — see the productivity trap.

See Also

Graph View