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notdocs vs Obsidian

Both keep markdown files. What differs is where they live, who edits them, and how.

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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 What follows describes Obsidian from its public documentation as of the date above; if something here is out of date, write to hello@notdocs.dev.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

notdocsObsidian
Where content livesA git repository, hosted on GitHub or a local folderA vault folder on your device
FormatMarkdown with YAML frontmatterMarkdown with YAML properties
EditingWeb appDesktop and mobile apps
Sharing with othersOrganizations with members and guests; documents shared by link or published as a site on your own domainShared vaults through Obsidian Sync, or git through a community plugin
AgentsMCP server and CLI, with project tokens and save-time mergesCommunity plugins and direct file access
Structured viewsQuery blocks as boards, tables, lists, calendars and galleriesBases, Dataview and other plugins
Links[[wikilinks]] as Obsidian writes them and markdown links, with backlinks that survive a moveWikilinks and a graph view
Extending itCustom types and templates in the repositoryA 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.