| note.md | Obsidian | |
|---|---|---|
| Storage | Plain markdown files, local | Plain markdown files, local |
| Price | Free, open source | Free (closed source); paid Sync/Publish |
| Reading AI documents | Core workflow: clean reading view, marks kept | A general editor; possible via setup |
| Annotations | Sidecar .note.md — source stays clean | Inline edits, or community plugins |
| Agent support | Built in: AGENTS.md conventions, block citations, annotations as agent input | Via plugins and DIY (a popular pattern) |
| Outliner | Native .note.md outline view | Via plugins; Obsidian is page-oriented |
| Plugin ecosystem | Small, out-of-process, capability-gated | Enormous — thousands of community plugins |
| Mobile | Not yet (macOS first) | Excellent iOS/Android apps |
| Interop | Vault opens in Obsidian | Vault opens in note.md |
The honest take
If you love Obsidian, keep it — seriously. It's the most successful file-over-app editor ever made, its plugin ecosystem is unmatched, and pointing Claude Code at an Obsidian vault is one of the great DIY patterns of the decade. note.md's vault format is deliberately Obsidian-compatible, because we believe the same thing they do: your files should open anywhere.
The difference is what happens out of the box. Obsidian is a general-purpose toolbox you assemble: to get the AI reading loop working you wire up plugins, conventions, an agent config, and hope the pieces stay compatible. note.md ships the loop as the product: agents write documents, you read them in a view built for judgment, your highlights land in a sidecar .note.md that never pollutes the source, and every agent that visits your vault reads your margins first. No assembly.
The sidecar is the real fork in the road. Obsidian's annotations live inside the document — fine for notes you wrote, awkward for documents an agent generated and might regenerate. note.md separates the regenerable (the AI's text) from the irreplaceable (your judgment), file by file.
Use both
This isn't a divorce. A note.md vault is a folder of markdown: open it in Obsidian for graph view and mobile capture, open it in note.md for the reading-annotation loop and agent workflows. Two clients, one source of truth. That's the whole point of files.
Choose one (or don't)
- Choose Obsidian if you want maximum plugins, mobile apps, and graph view — and enjoy assembling your own AI workflow.
- Choose note.md if your day is increasingly reading what agents wrote, and you want annotations-as-data and agent conventions without any assembly.
- Use both on the same vault. Files don't make you choose.
FAQ
Can I open my note.md vault in Obsidian?
Yes. A note.md vault is plain markdown with filename-resolvable [[wikilinks]], deliberately kept Obsidian-compatible. Sidecar .note.md files appear as ordinary notes there.
Do I have to leave Obsidian to use note.md?
No. Point both apps at the same folder. Many users keep Obsidian for mobile capture and graph view, and use note.md for reading AI documents and annotating.
What is a sidecar annotation?
When you highlight or comment on xxx.md in note.md, your marks are saved to a companion file xxx.note.md. The original document stays clean and regenerable; your judgment becomes separate, searchable data.