
Imagine you have been tending a garden for years — planting seeds, pulling weeds, carefully arranging beds. Then one day a skilled assistant arrives who already knows your garden by heart: where the roses go, how the soil prefers to drain, which paths you walk most often. You no longer need to explain the layout every time. You just say what you want to grow, and together you make it happen. That is roughly what happened when I connected an AI agent to my Zettelkasten.
From Manual Craft to Assisted Flow
For years I have maintained a plain-text Zettelkasten built on Markdown files, managed with my own open-source toolkit tools4zettelkasten [1]. Staging notes, assigning canonical filenames, reorganizing branches, updating internal links — all of these tasks required running Python scripts from the command line and keeping the conventions in my head.
That changed when I set up Claude Cowork with a direct connection to my Zettelkasten through an MCP server. MCP — the Model Context Protocol introduced by Anthropic [2] — acts like a standardized plug between an AI model and external tools. In my case the MCP server wraps the Python scripts I already had, so the agent can stage files, reorganize notes, search the archive, and analyze its structure without me typing a single command.
On top of that, I created a dedicated skill — a reusable set of instructions that tells the agent exactly how I want my Zettelkasten maintained. Think of a skill as a recipe card the agent consults every time it works with my notes. It knows the naming conventions, the ordering logic, the linking rules. I no longer have to re-explain my workflow in every conversation.
The result? My head is free. I stopped thinking about the technicalities and started thinking about the ideas.
Rethinking Note-Making in a Practical Context
The Zettelkasten community often emphasizes the importance of rewriting notes in your own words — the step from “note-taking” to “note-making” that Anne-Laure Le Cunff describes so well [3]. And there is deep truth in that principle. But I have found that for my particular context, the process looks a bit different.
I do not work in academia. I work in IT, where I need to quickly grasp new concepts — GPU architectures, cloud infrastructure patterns, emerging frameworks — and bring them into practice. My Zettelkasten is less a publishing engine and more a learning engine: a tool for decomposing complex ideas into pieces I can understand and recombine.
What matters to me is not the polished reformulation of a thought on paper. What matters is the depth of engagement with the material itself. And that engagement, I discovered, can happen away from the keyboard entirely.
Learning on the Move with Voice Mode
Here is where my workflow took an unexpected turn. I started using ChatGPT’s voice mode during car rides and walks. Instead of sitting at a desk reading papers, I have conversations with the AI — asking it to explain what distinguishes a GPU from a CPU, what the different GPU types are, how tensor cores work, and so on.
These are not passive lectures. They are dialogues. I ask follow-up questions, challenge answers, request analogies. By the time I park the car, I have spent thirty or forty minutes actively engaging with a topic that was new to me an hour earlier.
After such a conversation, I ask the AI to distill the essence into a concise note — just a few lines that capture the core insight. Sometimes it takes three or four attempts to arrive at a formulation that truly reflects what I have learned. All of this happens while I am on the move, turning otherwise idle time into deep learning sessions.
From Voice to Zettelkasten: The Integration Pipeline
Once I have a draft note, the AI helps me bring it into the right shape:
- Formatting: The note is converted into the Markdown structure my Zettelkasten expects — proper headings, clean syntax, correct link format.
- Source enrichment: References from my literature management are added, so every claim remains traceable.
- Staging and integration: The agent uses the MCP tools to stage the note, assign a canonical filename, and place it in the right position within the Zettelkasten’s ordering.
What used to be a sequence of manual steps — formatting, naming, moving files, updating links — now happens in a single conversation with the agent.
Retrieval That Goes Beyond Keywords
Finding the right note in a growing Zettelkasten has always been a challenge. The traditional navigation tools — following sequences of notes forward and backward, tracing cross-references through links — work well when you already know roughly where to look. But they have their limits. As the archive grows, you cannot hold the full map in your head, and keyword searches only help when you remember the exact term you used. Knowledge, however, does not always organize itself around keywords.
That is why I built a RAG system (Retrieval-Augmented Generation) on top of my Zettelkasten. Instead of relying on exact matches, the system understands the semantic meaning behind a query. When I ask “What do I know about scaling machine learning infrastructure?”, it surfaces relevant notes even if none of them contain those precise words.
This turns the Zettelkasten from a static archive into something closer to a conversation partner — one that has read all your notes and can point you to the ones that matter right now.
The Structure Remains — The Work Transforms
What surprises me most is how little has changed on the surface. My Zettelkasten still consists of numbered Markdown files in a folder. The tools4zettelkasten scripts still handle the heavy lifting of renaming, linking, and reorganizing. The hierarchical ordering that gives my notes their structure is exactly the same.
Yet the experience of working with the system has fundamentally shifted. The friction is gone. The cognitive overhead of maintaining the system has been absorbed by the agent. And that freed-up mental energy flows directly into what the Zettelkasten was always meant to support: thinking deeply about ideas.
If you are running a Zettelkasten — whether digital or analog — I encourage you to explore how AI tools can take over the mechanical parts of your workflow. Not to replace your thinking, but to clear the path for more of it. The garden still needs a gardener. But a good assistant can make the gardening a lot more joyful.
Sources
[1]: tools4zettelkasten on GitHub
[2]: Anthropic, ‘Model Context Protocol (MCP)’, 2024. https://modelcontextprotocol.io/
[3]: Anne-Laure Le Cunff, ‘From Note-Taking to Note-Making’, Ness Labs. https://nesslabs.com/from-note-taking-to-note-making
[4]: Sönke Ahrens, How to Take Smart Notes (Books on Demand, 2017).



















