How I Use AI to Manage My Obsidian Vault
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Knowledge Management2026-03-08· 7 min read

How I Use AI to Manage My Obsidian Vault

My Obsidian vault has 3,200+ notes. AI agents organize it, surface relevant connections, generate summaries, and turn my notes into published content automatically.

#Obsidian#AI agents#PKM#note-taking#knowledge management#productivity

I've got 3,247 notes in my Obsidian vault. Ideas, resources, meeting notes—everything I’ve learned in the past three years lives there.

Without AI? Just a graveyard of forgotten notes. With AI? A living knowledge system that:

  • Organizes new notes automatically
  • Surfaces relevant connections when you're writing
  • Generates rediscovery prompts showing me old insights
  • Converts my notes into polished content

My second brain isn't just storing info; it helps me think.

Let’s dive into the exact AI systems I built on top of Obsidian.

Why Obsidian + AI Is Perfect

Obsidian alone: Good for storage, bad at making sure you use those notes.
AI layer changes everything:

Because Obsidian stores everything as plain markdown files in a local folder, you can:

  • Run scripts to process your vault
  • Use AI to generate new content and insights
  • Build automations that read and write notes

Unlike Notion or Roam (cloud-based, proprietary), Obsidian gives you full control of your data. Perfect for AI integration.

The Five AI Agents Running My Vault

Agent 1: The Auto-Organizer

Problem: I dump notes quickly; organizing them later? Never happens.

Solution: AI organizes automatically.

When I create a new note:

  1. Reads the content
  2. Analyzes using OpenAI
  3. Suggests tags and related folders
  4. Identifies related notes based on semantic similarity
  5. Auto-creates links

Script runs via Keyboard Maestro trigger:

import openai

def organize_note(note_path):
    content = read_note(note_path)
    
    analysis = openai.ChatCompletion.create(
        model="gpt-4o-mini",
        messages=[{
            "role": "user",
            "content": f"Analyze this note: {content}"
        }]
    )
    
    add_tags(note_path, analysis['suggested_tags'])
    suggest_links(note_path, analysis['related_notes'])

Every note gets organized automatically.

Agent 2: The Connection Finder

Problem: Connecting notes is hard. I forget what's in 3,247 notes.

Solution: AI finds connections for me.

When writing:

  1. Monitors clipboard or editor
  2. Searches vault for relevant notes
  3. Surfaces them in a sidebar

Example: Writing about "morning routines." My agent shows:

  • Note from 2024
  • Highlight from Atomic Habits
  • Meeting note with productivity coach

All useful, all new.

Agent 3: The Daily Rediscovery

Problem: I have insights that I forget.

Solution: AI surfaces old notes daily.

Every morning, my vault's daily note includes:

  • Random old notes (to spark connections)
  • Notes from a year ago
  • Important but neglected notes
  • Notes related to current projects

Script runs at 6 AM:

def create_daily_rediscovery():
    today = datetime.now()
    
    random_notes = sample_notes(older_than_days=90)
    year_ago_notes = get_notes_from_date(today - timedelta(days=365))
    neglected_notes = get_notes(min_backlinks=5, not_opened_in_days=30)
    related_notes = find_relevant_notes(get_current_projects())
    
    add_to_daily_note(format_rediscovery(
        random_notes, year_ago_notes, neglected_notes, related_notes
    ))

Keeps my knowledge fresh.

Agent 4: The Content Generator

Problem: I have tons of notes but need to publish content. Manually connecting the two is slow.

Solution: AI converts notes to publishable content.

I tell it: "Create a blog post outline about AI agents using my vault notes"

It:

  1. Searches for relevant notes
  2. Extracts key points
  3. Synthesizes into a coherent outline

Output example:

# AI Agents for Content Creators - Outline

## Introduction
- Personal story
- Hook

## What Are AI Agents
- Definition
- Key features

## Why Creators Need Them
- Pain points
- Statistics

## How to Get Started
- First automation
- Tools needed

I can then expand and publish.

Agent 5: The Smart Search

Problem: Obsidian's search is keyword-based; I often forget exact words.

Solution: AI semantic search.

I ask questions like:

  • "What did I learn about morning routines?"
  • "Notes about failed experiments"

AI searches for meaning:

def semantic_search(query):
    query_embedding = get_embedding(query)
    
    results = find_similar(query_embedding, vault_embeddings, threshold=0.7)
    
    answer = openai.ChatCompletion.create(
        model="gpt-4o",
        messages=[{
            "role": "user",
            "content": f"Based on these notes: {results} answer: {query}"
        }]
    )
    
    return answer

AI provides specific, useful answers.

The Technical Setup

Tools I use:

  • Obsidian (free)
  • Python scripts (free)
  • OpenAI API ($20-30/month)
  • Keyboard Maestro ($36 one-time)
  • Hazel ($42 one-time)
  • Git (free)

Architecture:

  1. Obsidian vault = folder of markdown files
  2. Python scripts monitor the folder
  3. When changes detected, run AI processing
  4. Write results back to vault as new notes or metadata

Key insight: Because Obsidian is just markdown files, you can manipulate them with any programming language.

Getting Started

Week 1: Basic Setup

  • Install Obsidian
  • Start taking notes (don't worry about organization yet)
  • Get comfortable with markdown and linking

Week 2: Add Auto-Organization

  • Set up Python environment
  • Build simple auto-tagging script
  • Test on new notes

Week 3: Add Connection Finding

  • Generate embeddings for existing notes
  • Build semantic search
  • Test finding related notes

Week 4: Add Rediscovery

  • Build daily note automation
  • Add random note surfacing
  • Refine based on what's useful

Month 2+:

  • Add content generation
  • Build custom workflows for your needs
  • Integrate with other tools

Don't try to build everything at once. Layer capabilities progressively.

The Philosophy

Your notes shouldn't be an archive; they should be a conversation partner.

AI amplifies thinking by:

  • Remembering what you’ve forgotten
  • Connecting related ideas
  • Synthesizing across learned concepts
  • Suggesting new insights

Obsidian gives you a place to think. AI makes that thinking compound over time.

My 3,247 notes aren't just sitting there; they’re actively contributing to everything I create.

Build your AI-powered second brain with Obsidian and my tools at axon.nepa-ai.com.

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