Markdown is a text file with a few punctuation conventions. That is the whole appeal. A plain .md file can be opened in many editors without the original application. Application features around that text, such as block properties, queries, whiteboard layouts, and attachment references, can still require migration work.
Markdown is also a readable text format for assistants. Access permissions and a working connection determine whether a particular assistant can use those files.
How the category breaks down
Writing apps such as iA Writer, Typora, and Zettlr focus on editing Markdown files. Knowledge bases add organization and retrieval, with different storage choices: Obsidian uses local files, Joplin and Bear provide library exports, and Logseq DB uses SQLite while OG remains a separate file-graph product. Hosted knowledge bases such as Hjarni expose notes over an official remote MCP server.
If local storage or encrypted sync is required, compare those options directly. Bear also has a web beta; that does not make its documented local macOS MCP remotely hosted. Logseq DB and OG have different export behavior. Keep storage, sync, human editing, and assistant access as separate checks.
The part most roundups skip: can your AI read it?
A compatible local agent can read authorized Markdown files directly, or use a product CLI. Obsidian offers an official CLI. MCP is another connection method: it exposes specific tools for searching, reading, creating, or updating notes.
Check who maintains the server and where it runs. Joplin, Bear, and Logseq DB document official local MCP. A cloud assistant cannot directly open a localhost endpoint on your laptop; it needs a separately reachable bridge. Hjarni provides an official hosted endpoint, so you do not have to run that bridge yourself.
Then confirm the tools and permissions in the actual client. See the MCP note app page for a sourced per-app breakdown.