Johnny Decimal in Obsidian Without Folders

The Johnny Decimal website has a note that Obsidian was “too difficult” to make work with the system. I understand why. The standard implementation assumes physical folders, and Obsidian’s folder-based approach creates friction that compounds over time.

But there’s another way to run it. No folders at all — just numbered note titles, index notes, and links. Once I switched to this approach, Johnny Decimal and Obsidian stopped fighting each other.

Why folders cause problems in Obsidian

The original Johnny Decimal method pairs a numbered index with the file system: your folders mirror your areas and categories, everything has a numbered address, and the index tells you where things live.

In Obsidian, this breaks down as soon as you want to restructure. Moving a note to a new folder risks breaking links. Renaming a folder means updating every reference to it. And in the first few months of using any organizational system, restructuring is constant — you’re still figuring out what your actual categories are.

Physical folders lock in decisions you aren’t ready to make yet.

Index notes as virtual folders

The alternative is to build the structure in notes rather than in the file system.

Each category gets an index note. “30.00 Entertainment (index)” is a note that contains links to everything in that category: [[32.01 Books I've read]], [[32.02 Films]], [[32.03 Albums]]. The index note is the folder.

This changes the cost of restructuring. Moving something from one category to another means updating a link in one note and renaming a file — both of which Obsidian handles automatically. No broken links, no folder migration.

The index and the content also live in the same environment. In the classic Johnny Decimal setup, the index is separate from the file system, and navigating between them requires switching contexts. In Obsidian, opening an index note puts you one click away from any item in that category.

What the numbers are actually for

If you’re not using folders, you might wonder whether the numbers serve any purpose. They do — but the purpose is different from what the folder version uses them for.

Obsidian’s Quick Switcher (⌘+O) lets you navigate by typing part of any filename. Numbers make this fast in a specific way: they’re unique and language-independent. Typing “32” immediately filters to everything in that category. No translation overhead, no trying to remember which keyword you used.

After using a system for a while, a handful of frequently-used numbers become reflexive. You stop thinking “where is that note” and start thinking “32” — and you’re there. The number becomes a shortcut that doesn’t require remembering the exact title.

Don’t put everything in it

The most important thing I’ve learned from using Johnny Decimal in Obsidian: don’t try to manage all your notes with it.

Johnny Decimal works well for stable, reference-type information — health records, financial documents, project archives, configuration notes, anything that doesn’t change much and needs a permanent address.

It doesn’t work well for ideas in progress. Evergreen notes, developing thoughts, half-formed observations — these need to grow and connect organically. Assigning them fixed addresses before they’ve stabilized creates friction rather than clarity.

A useful test: is this note a record or a thought? Records benefit from a permanent address. Thoughts benefit from being linked into wherever they’re relevant at the moment.

Start with fewer numbers than you think you need

When beginning, the temptation is to plan the full system upfront — all ten areas, subcategories assigned in advance, everything numbered before you start filing.

This doesn’t work. You don’t know what your actual categories are until you’ve been using the system for a few months.

A better approach: start with just the top-level areas. ”10s: life logistics. 20s: guitar. 50s: work.” Run that for a few weeks. Only assign sub-numbers once you know what actually belongs there and how you naturally think about it.

The whole point of Johnny Decimal is to reduce the cognitive overhead of deciding where things go. That works best when the structure reflects how you actually think — which you can only discover by using it, not by planning it in advance.

The Japanese version of this page goes deeper into specific implementation details: 日本語版 →