Folders or tags for your Markdown notes?

Checked November 2026 against Obsidian's help on tags. Coffee isn't affiliated with Obsidian.

Use both, for different jobs. A folder says where a note lives, and a note can only be in one. A tag says what it's about, and a note can have several. For most people, a handful of shallow folders, tags written in each note's front matter, and a few pinned notes cover everything, and the argument over which is better goes away.

Here's how I'd set it up, and why the choice matters more with plain files than in an app with a database.

Why the choice matters with files

When your notes are Markdown files, a folder isn't just a label in an app. It's a real folder on disk, and every other tool sees it: Finder, Git, a backup, a script, an AI tool reading your notes. Tags are different. They live inside the file, and each app decides whether, and how, to read them.

That gives you a simple rule. Put the things that need to work everywhere into folders, and the things that are only about finding notes into tags.

What folders are good for

• Things that are separate in real life. Work and personal. One client and another. A book you're writing and everything else.
• Things other tools need to see. A folder you back up somewhere else, a folder that's a Git repository, a folder you'll turn into a book.
• Archiving. Moving finished notes into an Archive folder keeps the rest short.

Where folders go wrong is depth. When a folder sits five levels down, every new note comes with a small decision about where it goes, and you start keeping notes in the wrong place to avoid making it. Notes that belong in two places end up copied, or in neither.

What tags are good for

• Things that cut across folders. A tag like idea or waiting can sit on a work note and a personal one.
• Status. draft, todo, done. These change, and changing a tag is quicker than moving a file.
• A note that belongs in two places. It gets two tags instead of two copies.

Where tags go wrong is number. If every note gets new tags made up on the spot, you end up with meeting, meetings and mtg, and none of them find everything. A short list you actually reuse is worth more than a long one.

Where to write tags

There are two common ways. Inline tags are written in the text, like #meeting. Front matter tags go in a block at the top of the file:

---
tags: [work, planning]
---

Obsidian reads both, and its help says tags in front matter should always be written as a list. It also supports nested tags with a slash, such as #inbox/to-read.

If you want tags that travel between apps, front matter is the safer choice. The block is set apart from the writing, so a # in the middle of a sentence or a heading can't be mistaken for a tag, and Obsidian and Coffee both read it. There's more on how the block works in what front matter is.

A setup that works

1. Three to six folders at the top, for the parts of your life that really are separate. Add a folder inside one only when it has grown big enough to be annoying.
2. An Archive folder for anything finished.
3. A short list of tags, in front matter, for topics and status. Write the list down in a note if it helps.
4. Pins for the few notes you open every day, so they're always at the top whatever folder you're in.
5. One sort order per folder, by date for a folder of meeting notes and by title for reference notes.

If you're starting from one big folder, don't reorganise everything at once. Make the top folders, move notes as you touch them, and let the rest sit at the top level until they come up.

How Coffee shows folders, pins and tags

In Coffee, the sidebar shows your library as it is on disk.

Folders. Under Folders, Coffee lists the folders that hold notes, as a tree you can open and close, with a count of the notes inside each, including those in folders within it. Which folders are open is remembered on each Mac. Choose a folder to see the notes directly in it. Press ⌘N while you're looking at a folder and the new note goes there.

To move a note into another folder, use Move to… in the ··· menu beside the title, which also lets you make a new folder. When you move or rename a note in Coffee, its version history goes with it, and links to it are updated. Outside a note's own folder, the list shows which folder it's in, so two notes called "Notes" can be told apart.

Pins. Choose Pin Note from the Note menu, or Pin from a note's menu in the sidebar, and it appears under Pinned at the top, with its folder beside it. Unpin takes it off again.

Sort per folder. View > Sort Notes By offers Date Modified, Title or Date Created. Each folder remembers its own choice. The other lists, such as All notes, Today and tags, share one.

Where that's kept. Pins and sort choices are saved in .coffee/layout.json at the top of your notes folder. That way they go with the folder through iCloud Drive or Git, and Coffee never adds a file among your notes. A move or rename inside Coffee updates them, so a pin follows its note.

Tags. Coffee reads tags from a note's front matter, and only from there. It accepts tags: [work, planning], tags: work, or a list with one tag per line. A #word in the text stays as text. Tags appear under Tags in the sidebar, and Tags… in the Note menu edits them for you, writing the front matter if the note doesn't have any yet. If you're coming from an app with inline tags, they won't show up in Coffee until they're in front matter.

Coffee can also make one EPUB book from a folder or from a tag, a chapter per note, which is a good test of whether either is doing its job.

Coffee is Mac only, with macOS 15 or later. It's free for 14 days without a card, then €3 a month, €29 a year, or €79 once with two years of updates.

So which is it?

If you only want one: folders, kept shallow. They work in every app and every tool, with nothing to learn. Add tags when you notice a note that belongs in two places, or a status you keep wanting to search for. Add pins when you catch yourself opening the same three notes every morning.

Questions

Should I use folders or tags for notes?

Both. Use a few shallow folders for where a note lives, and tags for what it's about, since a note can only be in one folder but can have several tags.

How many folders should I have?

Few, and shallow. Three to six at the top level is plenty for most people, with a folder inside one only when it gets too big to scan.

Where should I put tags in a Markdown file?

In the front matter at the top, as tags: [work, planning]. It's kept apart from your writing, so a # in a sentence won't be mistaken for a tag, and both Obsidian and Coffee read it.

Does Coffee read #tags in the text?

No. Coffee reads tags from a note's front matter only. A #word in the text stays as ordinary text.

Where does Coffee keep pins and sort order?

In .coffee/layout.json at the top of your notes folder, so they go with the folder through iCloud Drive or Git. Which folders are open in the sidebar is kept on each Mac.