Give your AI agent an Obsidian knowledge base

Your agent’s built-in memory is small on purpose — it holds a compact set of facts that load into every session. But some knowledge is too big for that: how a tool works, the steps of a workflow you keep reusing, notes on a project. For that you want a proper knowledge base your agent can search on demand. This article sets up an Obsidian knowledge base for Hermes — a vault of Markdown notes the agent reads from and writes to — so your agent has a growing external brain alongside its memory.

What a vault is, and why use one

Obsidian is a free note-taking app built on a simple idea: your notes are plain Markdown files in a folder on your own machine. That folder is called a vault. There’s no proprietary database and no cloud lock-in — just readable text files you fully own.

That plainness is exactly why it pairs so well with an AI agent. Hermes can read and write those Markdown files directly, the same way it handles any other file. So the vault becomes a knowledge base your agent can consult and add to — the place for everything that doesn’t fit in its compact memory.

The division of labour is the point. Your agent’s memory is small and loads into every single session, so it’s reserved for frequently-used facts. The vault is for the long, detailed stuff you only need occasionally: how a particular tool works, a workflow’s exact steps, notes on each project. Memory is what the agent always carries; the vault is what it looks up when needed. Keeping the big knowledge in the vault stops it from crowding out the memory — which is a subject in its own right, covered separately in this series.

Installing Obsidian

This is the quick part, and honestly the fastest route is to just do it yourself rather than have the agent try. Go to obsidian.md, download the Windows installer, and run it. It installs like any normal desktop app — no account required, nothing to configure to get started.

Obsidian is free for personal use, runs entirely on your machine, and doesn’t need an internet connection to work. Once it’s installed, you’re ready to create the vault itself.

Where to put the vault

A vault is just a folder, so the only real decision is where to put it. When you first open Obsidian, it offers to create a new vault — point that at a folder you’ll remember and can reach easily. A dedicated folder under your user directory works well, for example:

C:\Users\YourUsername\Obsidian\KnowledgeBase

Write down the exact path — you’ll hand it to Hermes verbatim in the next step, so it has to match character for character. Pick a location that’s stable: somewhere you won’t move or rename later. Avoid putting it inside a folder that syncs or reorganises itself unpredictably. Once Obsidian creates the vault, it drops a hidden .obsidian configuration folder inside; leave that alone, it’s the app’s own settings.

Pointing Hermes at the vault

There are two separate things to get right here, and it helps to keep them apart: the skill that teaches the agent how to work with a vault, and the path that tells it where your vault actually is. The skill has a place in the app’s Capabilities list; the path does not — that one is a single line of config. Do both and the connection is complete.

1. Confirm the Obsidian skill is enabled

Hermes ships with a bundled note-taking skill for Obsidian — the saved procedure the agent follows to read notes, search them, and write new ones cleanly. You don’t build it; you just confirm it’s there. In the desktop app:

• Open Capabilities from the top-left of the app — this opens the list of skills.
• In the search box at the top, type obsidian. The skill appears in the filtered list.
• Make sure it’s enabled. If it’s listed and on, the agent already knows how to work with a vault.

Prefer the terminal? The same check is hermes skills list — look for obsidian under the note-taking category.

2. Tell Hermes where the vault lives

This is the part that catches people out: there is no field in Capabilities for the vault folder. Enabling the skill switches the behaviour on, but it never asks you for a path. That’s set with a single environment variable, OBSIDIAN_VAULT_PATH, which lives in Hermes’s .env file. On Windows that file is at:

%LOCALAPPDATA%\hermes\.env

Open that file in any text editor and add one line, using the exact path you chose earlier:

OBSIDIAN_VAULT_PATH=C:\Users\YourUsername\Obsidian\KnowledgeBase

Save it, then restart Hermes so it picks up the new value. That’s the whole connection. If you skip this step, the skill falls back to a default location — ~/Documents/Obsidian Vault — so if you created your vault somewhere else and never set the variable, Hermes will be looking in the wrong folder and quietly find nothing. Setting the path explicitly is what makes it reliable.

Prefer not to touch the config file?

Then let the agent do it. Tell Hermes plainly: “My Obsidian vault is at C:\Users\YourUsername\Obsidian\KnowledgeBase — set that as your knowledge base.” It can write the variable to its own .env for you. Either way, apply the pattern from the foundation article afterwards: have Hermes repeat back the path it will use and confirm it can list the vault’s contents, so you know the connection actually took before you rely on it.

Using it: the “summarise and save” habit

Here’s where the vault earns its keep, and it comes down to one habit. Whenever you’ve done something worth keeping — worked out how a tool behaves, settled on a workflow, researched a topic — ask Hermes to summarise it and save it as a note in the vault.

That single instruction does a lot. Hermes distils the useful part, writes it as a clean Markdown note, and files it in your vault. Do this consistently and your knowledge base grows on its own, capturing the things you’d otherwise have to re-explain or rediscover later. A good note usually includes:

• A clear title so it’s findable later.
• Links to related notes — in Obsidian you connect notes with [[double-bracket]] links, which build a web of related knowledge the agent can follow.
• The distilled point, not a raw dump — the summary is what makes it useful next time.

A concrete first test: after finishing any earlier article in this series, ask “summarise what we just set up and save it as a note called Hermes setup in the vault.” Then open your vault folder in Obsidian and confirm the .md file is actually there. Seeing that first note appear is how you know the whole chain — skill, path, write access — is working end to end.

Over weeks, this turns into a genuine second brain: when you ask Hermes about something you covered before, it consults the vault instead of starting from nothing. The “summarise and save” habit is small, but it’s what makes the whole thing compound.

Why an index makes it fast

One practical wrinkle worth knowing about. When your vault is small, Hermes can read notes directly and it’s fine. But as it grows to dozens of notes, having the agent read every note one by one to find something becomes slow and burns tokens.

The fix is an index: a single file — in practice a _meta/index.json in the vault — that maps every note’s title, tags, and links, so the agent reads one compact map instead of crawling every note. It’s the difference between checking a library’s catalogue and walking every shelf. This is the piece that keeps a large vault fast and cheap to use, and it’s worth setting up once the vault has more than a handful of notes.

Building that index (and refreshing it automatically) is a more technical topic with its own moving parts, so it gets a dedicated deep-dive article in this series. For now, know that the index is what makes a growing vault scale — and that Hermes can generate one for you when you’re ready.

Frequently asked questions

Can I set the vault folder from the Hermes settings screen?

Not the folder itself. Capabilities (top-left in the app) is where you enable the Obsidian skill — search “obsidian” at the top of the skill list — but there’s no folder-picker there for the vault path. The path is the OBSIDIAN_VAULT_PATH environment variable in Hermes’s .env file (%LOCALAPPDATA%\hermes\.env on Windows). You add that one line yourself, or you ask Hermes to write it. If you never set it, the skill defaults to ~/Documents/Obsidian Vault.

Why not just keep everything in the agent’s memory?

Because memory is small and loads into every session — it’s meant for compact, frequently-used facts. Long, detailed knowledge would crowd it out and inflate every prompt. The vault holds that material separately and the agent looks it up only when needed, keeping memory lean.

Do I need any Obsidian plugins or an MCP server for this?

No. Because a vault is just Markdown files in a folder, Hermes can read and write them with its normal file tools once it knows the path. Plugins and MCP servers are optional extras, not requirements for a working knowledge base.

What should go in the vault versus memory?

A rule of thumb: if it’s a short fact you want the agent to always know (your name, a standing preference), that’s memory. If it’s long-form knowledge you need occasionally (how a tool works, a project’s details, a workflow), that’s the vault.

How do I keep the vault from becoming a mess?

The “summarise and save” habit helps, because you’re storing distilled notes rather than raw dumps. Using folders for broad areas and [[links]] between related notes keeps it navigable. And once it grows, the index gives the agent a clean map regardless of how many notes there are.

What’s next

Your agent now has a knowledge base: a vault it can read, search, and grow. The habit to build is simple — after anything worth keeping, ask Hermes to summarise it and save it as a note. Over time that turns into an external brain that makes every future session smarter.

The next article is the technical companion: it shows how to build a vault index so the agent reads the whole vault in one call instead of crawling every note. This article is part of the Agentic AI series.