Chris EichlerAI-first Product
& Marketing

Obsidian — the brain for AI


Step 1: install and create your vault

  1. Download: grab the Obsidian app for Mac, Windows, or mobile → obsidian.md/download
  2. Create a vault: after opening, you create your first "vault". This is just a new folder on your computer where all your future notes are stored as text files.

Step 2: set the important defaults

Before you dive in, adjust two settings to save yourself future pain:

  • Auto-update links: Settings → Files and Links → enable "Automatically update internal links". When you later rename a note, all links to it update automatically — no broken connections.
  • Folder for attachments: define a default folder for new attachments. Prevents inserted images and files from cluttering your sidebar.

Step 3: create and link notes

The heart of Obsidian is linking ideas together.

  • New note: click the new-note icon and start writing.
  • Linking: to connect one note to another, type two opening square brackets [[ and start typing the note name. Close with ]].
  • Use placeholders: you can also link to notes that don't exist yet. When you later click the link (Mac: Cmd+Click, Windows: Ctrl+Click), the new note is created automatically.
  • Graph view: in "Graph View" you can see all these connections as an interactive web of nodes and lines.

Step 4: format text with Markdown

Obsidian uses Markdown for formatting. No complex menus — formatting happens as you type:

FormattingSyntaxResult
Heading# Text / ## Text / ### TextDifferent levels
Bold**Text** or Cmd/Ctrl + BBold
Italic*Text* or Cmd/Ctrl + IItalic
Highlight==Text==Highlight
Strikethrough~~Text~~Struck through
Bullet list- TextBullet list
Numbered list1. TextNumbered list
Checklist- [ ] TextCheckbox
Block quote> TextIndented quote
Horizontal rule---Horizontal line
External link[Text](URL)Clickable link
Embed![[Notename]]Inline embed

Step 5: organising your notes

Avoid the beginner mistake of building complex folder hierarchies or installing complicated plugins from the start — or importing thousands of old notes at once.

  • Use folders sparingly: create big "buckets" (categories) for your notes and refine the folder structure only when it becomes truly necessary. Too many folders cause decision fatigue at filing time.
  • Use tags: apply tags with # to bundle notes by topic.
  • Maps of Content (MOCs): central hub notes that organise and link other notes on a topic. Better than rigid folder structures.

Obsidian + Claude Cowork — the perfect duo

Obsidian and Claude Cowork complement each other beautifully because both build on the same foundation: local markdown files on your computer.

Why they fit so well

Obsidian stores everything as .md files in a regular folder on your machine. Claude Cowork can access exactly that kind of folder — you simply pick your Obsidian vault as the working folder in Cowork. From there Claude can read, search, extend, and create new files directly in your vault.

What you can concretely do

  • Summarise notes: have Claude read multiple notes on a topic and produce a summary as a new MOC page.
  • Research and insert content: Claude can do web research and drop the results straight into your vault as a new Obsidian note — with proper Markdown formatting and internal links.
  • Tidy the vault: Claude can unify tags, find duplicate notes, suggest missing links, or propose a better folder structure.
  • Generate templates: ask for templates for recurring note types (meeting notes, project pages, reading notes).
  • Query your knowledge: ask Claude questions about your own notes — e.g. "What have I noted about topic X?" or "Summarise my meeting notes from last week."

How to set it up

  1. Open Claude Cowork on your desktop.
  2. Pick your Obsidian vault folder as the working directory (the folder that contains your vault).
  3. Done. Claude can now read every note in your vault and create new files.

💡 Tip: because Obsidian picks up files in real time, you see anything Claude creates or changes immediately — no restart, no sync, no cloud.

Manage CLAUDE.md and SKILL.md in Obsidian

Claude Code and Claude Cowork use special config files — CLAUDE.md and SKILL.md — written in markdown. That makes Obsidian the ideal editor for them.

What are these files?

  • CLAUDE.md lives in the .claude/ folder of your project and contains project-specific instructions for Claude: who you are, what tech stack you use, which code conventions apply, how Claude should respond. Basically a "briefing" for Claude, loaded automatically every session.
  • SKILL.md files define skills — specialised abilities Claude activates for specific tasks (e.g. creating documents, applying brand voice, writing learning content). Every skill has its own SKILL.md with instructions, rules, and examples.

Why Obsidian is perfect for it

  • Native markdown: CLAUDE.md and SKILL.md are plain .md files — Obsidian shows them natively with syntax highlighting, formatting, and live preview.
  • Linking: you can link your CLAUDE.md to other Obsidian notes. For example, create a note [[Tech Stack]] or [[Brand Voice Rules]] and reference them from CLAUDE.md.
  • Fast editing: changes to your CLAUDE.md take effect immediately — no deploy, no rebuild.
  • Build a skill library: drop all your skills as folders in Obsidian. Each skill folder contains its SKILL.md.

Practical setup

  1. Vault = project folder: use your project folder (the one with .claude/) as the Obsidian vault.
  2. Create a Skills MOC: make a Map of Content [[Skill overview]] that links all your skills.
  3. Use tags: tag your skill files with #claude-skill and your configuration with #claude-config.
  4. Create templates: make an Obsidian template for new skills with the standard structure of a SKILL.md.

Example folder structure

What a project folder that doubles as an Obsidian vault using multiple Claude skills could look like:

my-project/                          ← Obsidian Vault root
│
├── .obsidian/                       ← Obsidian settings
│
├── .claude/                         ← Claude configuration
│   ├── CLAUDE.md                    ← Project briefing for Claude
│   └── skills/                      ← All skills live here
│       ├── brand-voice/
│       │   └── SKILL.md
│       ├── content-writer/
│       │   └── SKILL.md
│       ├── docx/
│       │   └── SKILL.md
│       └── pdf/
│           └── SKILL.md
│
├── input/                           ← Raw material & sources
│   ├── briefings/
│   ├── transcripts/
│   └── research/
│
├── assets/                          ← Images, logos, media
│
├── docs/                            ← Finished documents & outputs
│   ├── proposals/
│   ├── reports/
│   └── content/
│
├── notes/                           ← Obsidian notes
│
├── MOCs/                            ← Maps of Content
│   ├── Skill overview.md
│   ├── Project dashboard.md
│   └── Content pipeline.md
│
└── templates/                       ← Obsidian templates

Why this structure works:

  • Input vs. output: input/ holds raw material, docs/ finished results. Claude can read from input/ and write to docs/.
  • Assets centralised: all media in one place. Obsidian shows images inline, Claude can embed them in documents.
  • Skills next to notes: the .claude/skills/ live in the same vault — you can edit them in Obsidian and see in the Graph View how they relate to your MOCs.
  • MOCs as navigation: instead of digging through folders, open your Map of Content and jump straight to the destination by link.

The advantage over cloud-based tools

Unlike Notion or Google Docs, there are no API limits, no sync problems, and no dependency on third-party integrations. Claude works directly on your files — fast, private, and without detours.

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Chris Eichler