Claude Code and Obsidian Vault Setup

Obsidian stores notes as local Markdown files inside a folder called a vault. When Claude Code runs in that folder, it can read files you approve and use a CLAUDE.md file for project instructions.

What this helps you do

Create a simple Raw, Wiki, and Output structure so source notes stay separate from cleaned knowledge and Claude-generated work.

Before you start

Install Obsidian and Claude Code. Obsidian's core app is free. Optional Sync and Publish services cost extra. Create a new vault for the material you want Claude to access. Do not place passwords, patient data, client secrets, or unrelated private files in it.

Terms to know

• Vault: a normal folder containing Obsidian notes and settings.
• Markdown: plain-text files ending in .md.
• CLAUDE.md: project instructions Claude Code loads as context.
• Raw: original notes.
• Wiki: cleaned reference notes.
• Output: generated deliverables.

Step-by-step

1. Create a new Obsidian vault.
2. Add folders named Raw, Wiki, and Output.
3. Put original notes in Raw. Keep source names and dates.
4. Add the CLAUDE.md file below at the vault root.
5. Open a terminal in the vault folder and start Claude Code.
6. Ask Claude to summarize one Raw note into Wiki, with links back to the source.
7. Ask a question that the vault cannot answer and confirm Claude labels it missing.

Copy this

Save this as CLAUDE.md in the vault root:

# Vault rules

- Treat `Raw/` as source material. Never rewrite or delete it.
- Save cleaned reference notes in `Wiki/`.
- Save drafts and deliverables in `Output/`.
- Cite the source filename and heading for factual claims.
- Separate facts from inferences.
- If the vault does not support an answer, write `Not found in this vault`.
- Ask before moving, renaming, deleting, or overwriting any file.
- Never read or expose files outside this vault unless I approve the exact path.

Then try:

Read Raw/[FILE]. Create Wiki/[TOPIC].md with a short summary, key facts, open questions, and links back to each source heading. Do not add outside facts.

Things to know

Claude Code does not develop permanent human-like memory from a vault. Each session has a fresh context window. CLAUDE.md, files, and Claude's separate auto-memory feature provide reusable context. Large vaults may not fit into one conversation, and Claude can miss or misread notes. Local Obsidian storage does not mean content stays local after you send it to an AI service.

If something goes wrong

• If Claude starts in the wrong folder, exit and reopen it from the vault root.
• If it cannot find a note, confirm the filename and use a relative path from the vault.
• If it changes Raw files, stop, review the Git diff or backup, and strengthen the no-edit rule.
• If the vault is too large, work by topic folder and ask Claude to list the files it actually read.

Final check

The setup passes when the Raw file stays unchanged, the Wiki note cites the right source, Output remains separate, an unsupported question is labeled missing, and no file outside the vault is accessed.