Notes pile up for years, and there's no way to ask them anything. Now there is: open Claude Code right inside your Obsidian folder and the agent reads your markdown notes directly, answers from them, connects ideas and tidies things up. No plugins, no embeddings, no indexing.
What you end up with
- A personal knowledge base in Obsidian: notes wired together with
[[links]], the files are yours (markdown on disk), zero vendor lock-in. - An agent that answers from YOUR notes and names the source files. The mechanics are unlike RAG plugins: Claude Code searches and reads the vault's files directly, the way it reads code — no vector databases, no reindexing.
- Rituals on autopilot: "saved an article → a summary landed in the base", a weekly review built from your daily notes, finding non-obvious connections between topics, clearing the Inbox with a single command.
- CLAUDE.md — the base's "constitution": your rules for structure and formatting, which the agent re-reads at the start of every session.
What you'll need
Tools from this library (by name): Claude Code (the second brain's engine), the obsidian-skills skills (so the agent doesn't break wikilinks, callouts or Bases — see the obsidian-skills card), the "Summarise an article/video + what to apply" prompt (for filling the base). If you need full privacy, look at the "Private AI over your own files (local RAG)" and "Local / private" combos: that's the alternative offline route. Outside the library: Obsidian itself — free with no restrictions, including work notes (Sync is optional: the files are on your disk anyway). Accounts, money, hardware:
- Obsidian — $0. Claude Code — a Claude Pro subscription ($20/month, Claude Code included), Max, or Console API credits.
- Hardware: anything — the thinking happens in Anthropic's cloud, only the files live locally. No GPU needed.
Step by step
- The Obsidian vault. Tool: Obsidian. What to do: create a vault, write 3-5 notes and wire them together with
[[links]]; keep folders to 1-2 levels ("Inbox", "Projects", "Reference") plus tags. How you know it worked: you can tell where a new note belongs within two seconds. - Install Claude Code. What to do:
curl -fsSL https://claude.ai/install.sh | bash # macOS / Linux / WSL
irm https://claude.ai/install.ps1 | iex # Windows (PowerShell)
Run claude in the vault folder and log in (a Pro/Max subscription or Console). How you know it worked: ask "what notes are in this base?" and the agent lists your files.
3. CLAUDE.md — the rules of the base. What to do: create a CLAUDE.md file at the root of the vault (the /init command generates a draft — then edit it to taste). Write down: the folder structure, the note format (properties, tags), rules like "new things go in the Inbox" and "answer only from my notes and name the source files". The agent re-reads CLAUDE.md every session. How you know it worked: you ask "create a note about X" and it lands in the right folder in your format.
4. Skills for the Obsidian format. Tool: obsidian-skills (by kepano, Obsidian's CEO). What to do, inside a claude session:
/plugin marketplace add kepano/obsidian-skills
/plugin install obsidian@obsidian-skills
How you know it worked: [[wikilinks]], callouts and Bases in new notes open in Obsidian without broken syntax.
5. Filling the base with AI. Tool: the "Summarise an article/video + what to apply" prompt. What to do: instead of pasting whole articles, put in a distillation:
Write a summary for my knowledge base from this material: <link/text>.
Markdown format: 1) the gist in 3-5 bullets; 2) key ideas and terms;
3) what I personally should apply; 4) 3-5 tags. Wire it up with [[links]]
to related notes in the base, if there are any.
How you know it worked: the base holds a distillation with a "what to apply" section and links, not a raw copy of the article. 6. Working rituals. What to do: run the scenarios you set all this up for:
Answer from my notes: "<question>". If it isn't in the base, say so plainly.
Name the source files.
Read this week's daily notes. Pull together: what got done, what stalled,
which 3 topics keep coming up. Write it as a Weekly review note in "Reviews"
with links to the sources.
How you know it worked: the answers lean on your notes and name the files; the review shows up in the vault as a finished, linked note.
Free path vs fast (paid) path
Obsidian is free either way. The question is who does the thinking over the base.
| Aspect | Claude Code (this combo) | Local RAG (Ollama + a plugin) |
|---|---|---|
| Mechanics | the agent reads files directly | embeddings + vault indexing |
| Can change the base | yes: writes, edits, tidies up | no: search and answer only |
| Privacy | notes go to Anthropic's cloud | everything stays on your machine |
| Quality on hard questions | higher | lower, depends on your hardware |
| Software cost | from $20/month (Pro) or API | $0, but a GPU or Apple Silicon helps |
Personal notes, NDA work, medical records — go with the local stack (the "Local / private" combo). For everything else Claude Code is noticeably smarter and, unlike a plugin, doesn't just answer but does hands-on work in the base: writing, editing, tidying.
Common problems and fixes
- The agent breaks wikilinks, callouts or Bases. Plain markdown is not the Obsidian format. Install obsidian-skills (step 4) and pin the note format down in CLAUDE.md.
- It "can't see" the notes or the rules. Run
claudefrom the root of the vault: CLAUDE.md and the files are picked up relative to the current folder. - "Read the whole base" across 2,000 notes. Context is finite: ask it to search by topic or folder and break tasks up. Keep CLAUDE.md short — the official docs suggest up to about 200 lines, beyond that the agent follows the rules less reliably.
- The agent edited the wrong thing. It changes real files: keep the vault in git (or back it up) and review edits before approving them — Claude Code asks permission for changes by default.
- Secrets going to the cloud. Everything the agent reads is sent to Anthropic's API. For NDA and personal material, take the local route (see the table above).
- You hit the Pro limits. Long analyses of a big vault burn through the limit fast; break tasks up or look at Max/API.
- The base turns into a dump. The Inbox rule from step 1 plus a weekly "clear the Inbox following the CLAUDE.md rules" command to the agent — that's now one sentence instead of an evening of manual cleanup.
Time and money
- Time: the vault and its structure take 30-60 minutes; installing Claude Code, writing CLAUDE.md and adding the skills is another 20-30 minutes.
- Money: Obsidian — $0 (free with no restrictions). Claude Code — from $20/month (Claude Pro, Claude Code is included in the subscription) or API credits. The free private alternative is the local stack from the "Local / private" combo.
- Honestly: a second brain is valuable because of what accumulates in it — it's the habit of filing distillations, not a one-off setup. Claude Code takes the routine off your hands (summaries, reviews, connections, cleanup), but what goes into the base is still your call.