The difference in one line
Obsidian is a desktop and mobile editor for a folder of markdown on your device. notdocs is a web workspace over a folder of markdown in a git repository, with an MCP server and a CLI so your coding agents edit the same files.
Both keep your notes as plain markdown you own, so neither locks you in. What follows describes Obsidian from its public documentation as of the date above; if something here is out of date, write to hello@notdocs.dev.
Side by side
| notdocs | Obsidian | |
|---|---|---|
| Where content lives | A git repository, hosted on GitHub or a local folder | A vault folder on your device |
| Format | Markdown with YAML frontmatter | Markdown with YAML properties |
| Editing | Web app | Desktop and mobile apps |
| Sharing with others | Organizations with members and guests; documents shared by link or published as a site on your own domain | Shared vaults through Obsidian Sync, or git through a community plugin |
| Agents | MCP server and CLI, with project tokens and save-time merges | Community plugins and direct file access |
| Structured views | Query blocks as boards, tables, lists, calendars and galleries | Bases, Dataview and other plugins |
| Links | [[wikilinks]] as Obsidian writes them and markdown links, with backlinks that survive a move | Wikilinks and a graph view |
| Extending it | Custom types and templates in the repository | A large plugin and theme ecosystem |
Pick notdocs when
- The notes are a team's, not only yours. People sign in, see the same repository, and their saves become commits.
- The docs are about code. They sit in the repository they describe and travel with its branches and pull requests.
- Agents write alongside you. An MCP client lists, reads, searches and updates documents through the same operations as the app, and a merge keeps its edit from overwriting yours. See Agents.
- You want typed documents. A task has a status, a decision has a date, and the schema checks them.
Pick Obsidian when
- It is your own knowledge base. Obsidian is built for one person thinking in notes, with a graph of links between them.
- You want a native app that works offline on every device.
- You depend on plugins and themes that notdocs has no equivalent for.
Using both
They can share a folder. Point an Obsidian vault at the docs/ folder of a repository that notdocs serves, and edits from either show up in the other: the local daemon watches the folder, and the hosted service picks up whatever you push. Obsidian's wikilinks, embeds and callouts work as they are; the importer rewrites wikilinks to markdown links only if you ask it to. See Switch from Obsidian.