Obsidian Mastery February 20, 2026
Folders vs. Links: The Design Decision That Changes Everything
This is Part 2 of the Obsidian Mastery Series. , Part 1 | Part 3,
For the first six months of using Obsidian seriously, I organized almost everything with folders. I built a hierarchy. I moved notes. I renamed folders when the categories felt wrong, which was often. At one point I had fourteen top-level folders and could not tell you what was in any of them without opening them.
I was organizing my confusion, not my thinking. I did not realize that until I started linking instead of filing.
The choice between folders and links is not a preference question. It reveals something important about how ideas actually work, and building the wrong structure into your vault is one of the easiest ways to make Obsidian feel like it is working against you.
What Folders Are Good At
Folders are good at imposing pre-determined order on material that genuinely belongs in stable, distinct categories. Project files with clear phases. Reference material in well-defined domains. Content that has a natural home and stays there.
Folders also map onto how most people’s brains have been trained to organize information, file cabinets, library systems, computer directories. There is cognitive familiarity that reduces the overhead of learning a new paradigm. That matters.
What Folders Are Bad At
Folders are bad at representing the actual structure of ideas, which is almost never hierarchical. Ideas do not live in one place. An insight about creative confidence might belong in your personal development notes, your writing practice notes, your workshop design notes, and your coaching practice notes simultaneously. Folders require you to choose one location. That choice is always a simplification and often an impoverishment.
Folders are also bad at handling ideas whose categories are not yet clear, which is most ideas at the moment of capture. When you force categorization too early, you file things according to what they look like when they arrive, not what they turn out to be. Important ideas often need time to reveal what kind of idea they are.
What Links Are Good At
Links represent genuine relationships between ideas, relationships that cross the boundaries of any folder structure. A link says: these two things are connected, and that connection is worth preserving. Unlike a folder, a link does not claim exclusive ownership. A note can be linked from anywhere without moving. The idea exists in one place; its connections extend everywhere.
Links are also better at supporting serendipitous discovery. When you follow links during a review session, you encounter connections you did not plan, notes that speak to each other across months of separation. This is the behavior that makes people describe Obsidian as a thinking tool rather than just a storage tool. It emerges from linking, not from folders.
The Decision Rule
Stop debating which approach to use. Use each where it is genuinely strong.
Use folders for: your Inbox, your active projects, your templates, your archived material. These categories are real and relatively fixed. Folders serve them well.
Use links for: everything else, connecting ideas across areas, building topic maps from the bottom up, preserving relationships that cross categorical boundaries.
The underlying principle: your organizational system should reflect the structure of your thinking, not impose a structure that simplifies it past usefulness. Folders are a simplification that is sometimes worth making. Links are a complexity that is almost always worth embracing.
The Exercise That Makes It Click
This week, pick five notes from your vault. For each one, ask: could this belong anywhere else? Could it speak to something in a completely different area of my vault?
For every yes, add a link to the other note it connects to. Do not move the note. Just connect it. You will feel the difference immediately, the note goes from being an isolated artifact to being part of a conversation that extends beyond where it lives.
That feeling is the difference between a filing system and a thinking system. Once you feel it, the decision between folders and links stops being abstract.
Next in series: The 5 Note Types Every Thinking Person Needs →
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Pillar 04: Obsidian Mastery
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