Trilium Notes: Self-Hosted Knowledge Base with Hierarchical Notes

TL;DR — Quick Summary

Deploy Trilium Notes self-hosted knowledge base with hierarchical note trees, relation maps, code notes, E2E encryption, and scripting support.

Why Trilium Notes?

Note apps store notes. Trilium builds a knowledge base:

Hierarchical trees — Notes have children, forming deep structures.
Cloning — A note can exist in multiple tree locations.
Relation maps — Visual connections between concepts.
Code notes — Syntax highlighting for 30+ languages.
Scripting — Automate with server-side JavaScript.
End-to-end encryption — Protect sensitive notes.
Full-text search — Find anything instantly.

Prerequisites

Docker on any machine.
At least 256 MB RAM.

Step 1: Deploy with Docker

docker run -d \
  --name trilium \
  --restart=always \
  -p 8080:8080 \
  -v trilium-data:/home/node/trilium-data \
  zadam/trilium:latest

Access at http://your-server:8080.

Step 2: Note Types

Type	Use Case	Features
Text note	General writing, documentation	Rich text, markdown shortcuts
Code note	Scripts, configs, snippets	Syntax highlighting, execution
Relation map	Concept visualization	Visual node-and-edge diagrams
Book note	Long-form content	Ordered child notes as chapters
Canvas	Diagrams, mind maps	Freeform drawing
File note	Attachments	Store any file type

Step 3: Knowledge Base Patterns

Pattern	Structure	Use Case
Zettelkasten	Atomic notes + relations	Research, learning
Documentation wiki	Hierarchical sections	Team docs, SOPs
Personal journal	Date-based tree	Daily notes, reflection
Project tracker	Project → tasks → notes	Project management
Code library	Language → category → snippets	Developer reference

Trilium vs Alternatives

Feature	Trilium	Obsidian	Notion	Joplin
Self-hosted	Yes (server)	No (local files)	No (cloud)	Yes (sync only)
Hierarchical tree	Deep trees	Flat folders	Pages + DBs	Notebooks
Relation maps	Built-in	Plugin	No	No
Encryption	E2E per note	Vault-level	No	E2E
Scripting	Server-side JS	Plugins (JS)	Formulas	No
Code notes	Yes	Yes (markdown)	Code blocks	Yes
Cost	Free	Free / $8/mo sync	Free / $10/mo	Free

Troubleshooting

Problem	Solution
Sync not working	Check the sync server URL in desktop app settings; verify network connectivity
Note tree is slow	Large databases (>50k notes) may need PostgreSQL backend instead of SQLite
Can’t find a note	Use full-text search (Ctrl+S); check if note is in a protected subtree
Desktop app crashes	Update to latest version; check Electron compatibility with your OS

Summary

Hierarchical knowledge base — not just notes, but structured knowledge.
Relation maps visualize connections between concepts.
Cloning lets a note exist in multiple tree locations.
Self-hosted with E2E encryption for sensitive data.

Guide & Instructions

Estimated Time: 5m

Tools Needed:

Trilium Notes
Docker
Browser

Deploy with Docker

docker run -d -p 8080:8080 -v trilium-data:/home/node/trilium-data zadam/trilium

Create your first note tree

Open http://server:8080, create root notes, then add child notes to build a hierarchy.

Link notes with relations

Create relation maps to visualize connections between concepts.

Enable sync (optional)

Install the desktop app and configure sync with your server.

Frequently Asked Questions

What is Trilium Notes and who is it for?

Trilium is a self-hosted note-taking application designed for building personal knowledge bases. Unlike simple note apps, Trilium supports hierarchical note trees (a note can have child notes), relation maps (visual connections between notes), cloning (one note in multiple locations), and scripting. It's ideal for researchers, developers, and anyone building a structured knowledge system.

How is Trilium different from Notion or Obsidian?

Trilium is self-hosted (your data stays on your server), supports true hierarchical trees (not just flat folders), has built-in relation maps, and supports server-side scripting. Obsidian uses local markdown files but isn't self-hosted. Notion is cloud-only. Trilium offers end-to-end encryption for sensitive notes.

Does Trilium support markdown?

Yes. Trilium uses a rich-text editor with markdown shortcuts. You can also create dedicated code notes with syntax highlighting for 30+ languages. Notes can contain text, code, images, files, and rendered content.

Can I access Trilium from my phone?

Yes. The web interface works on mobile browsers. There's also a desktop app (Electron) that syncs with the server. The mobile experience is responsive but optimized for desktop.