Molecule Notes vs Obsidian

Your notes, with the other person in them.

An outline journal you write in together: each other's cursors, comments on the line they're about, and a graph of the links you've made. In a browser, on any machine.

Start writing

What Obsidian's docs say about sharing a vault

You will not see the other user's cursor, and their edits will only appear once the changes are synced.

From Obsidian Help: Collaborate on a shared vault

Obsidian is the best single-person notes app there is, and its documentation is unusually candid about where that stops. A shared vault is file sync between people, not writing in the same place at the same time.

That's a legitimate design choice. It's just not the one you need once you work with someone else.

In Molecule Notes, collaboration is a workspace you invite people to. You write in one place, on the day's page, and see each other's cursors as you type. Comments sit on the bullet they're about. Each person has a role, and a viewer can read without editing. There's no sharing page by page: you share the workspace.

Nothing needs filing, either. People give up on notes when deciding where each one goes takes longer than writing it. On a journal page every note is dated. Link a person, a book or a project with [[double brackets]], and every mention of it gathers on its page under Linked mentions.

20 collaborators at most.
"The maximum number of collaborators on a shared vault is 20 users."
Everyone gets the owner's permissions, bar one.
"All collaborators receive the same permissions as the vault owner, with one exception: only the vault owner can invite collaborators." There's no read-only access, and anyone you invite can delete anything in the vault.

Molecule Notes and Obsidian, side by side
Feature	Molecule Notes	Obsidian
Real-time co-editing	Yes: Live, with each other's cursors as you type.	No: "You will not see the other user's cursor…"
Read-only collaborators	Yes: Invite someone as a viewer. Roles are set per workspace.	No: Every collaborator has the vault owner's permissions, except inviting others.
Web app	Yes: Runs in a browser, and installs to your home screen.	No: Not available as a web application.
Notes as Markdown files you own	No: Stored as bullets in a database. Any page exports as Markdown.	Yes: Plain-text Markdown files in a vault, a folder on your own file system.
Daily notes and [[links]]	Yes: Every day has a page. Every mention gathers under Linked mentions.	Yes: Daily notes, internal links and Linked mentions, as core plugins.
Graph of linked pages	Yes: A graph view of the links you make.	Yes: A graph view of internal links, with color groups you set.
AI in the app	Yes: Name an agent on a line. It writes what it found under your line.	Not documented: None documented. About 900 community plugins are tagged AI.
Plugins	No: No plugin directory. Extensions are workspace agents you @mention on a bullet.	Yes: More than 7,600 community plugins.
Importing from other apps	Partly: Through MCP, by pointing an AI assistant at a vault.	Yes: An official Importer for Notion, Evernote, Apple Notes, OneNote, Roam Research, Logseq and more.

No web app

Obsidian isn't available as a web application; it runs as desktop and mobile apps. On a work laptop you can't install software on, or a borrowed computer, your vault isn't there.

Molecule Notes runs in the browser. Sign in and today's page is waiting, on whatever computer is in front of you, and you can install it to a phone's home screen. There's no native phone app, and it needs a connection to work.

Where the AI comes from

Obsidian isn't against AI. Its CEO, Steph Ango, publishes obsidian-skills, Agent Skills that teach an AI agent to use Obsidian's CLI and open formats, with 48.3k stars on GitHub. Inside the app, AI comes from the community: about 900 plugins are tagged AI, and putting a setup together from them is up to you.

Molecule Notes has one thing built in, and it isn't the main character. An agent is a colleague you call by name on a line. It reads your pages and the web, and writes what it found under your line. The rest of the page is still yours.

It also has an MCP server, so the AI assistant you already use can read and update your notes. A coding assistant can log the day's work on today's journal page, for example. Pages reach the assistant as Markdown with your [[links]] still in them, so it can follow one page to the next the way you would.

Getting your notes out of Molecule Notes

Any page exports as Markdown, with Copy as Markdown or Export as Markdown. It's one page at a time; there's no button that exports a whole workspace.

To take everything at once, connect an AI assistant to Molecule's MCP server. It can list your pages and read each one as Markdown, with its bullets and their nesting intact.

Bringing a vault in

There's no import screen and no drag and drop. Import goes through the MCP server: connect an AI assistant to Molecule Notes and point it at your vault.

It writes pages in bulk. Headings, lists and nesting become bullets. Obsidian's link forms work as they are: [[Note#Heading]], [[Note^block]], ![[Note]] and [[Note|shown text]] all point at Note, so Linked mentions build as the pages arrive. A note titled with a calendar day, like 2026-09-13, lands on that day's journal page.

Running the same import twice appends everything a second time rather than replacing it, so bring a vault in once.

Sources

Comparison verified September 2026.