Traditional note-taking apps treat notes as isolated documents:you create them, file them, and maybe search for them later. Connected notes apps work differently: every note can link to any other note, creating a web of knowledge where ideas reinforce each other.
This approach, inspired by the Zettelkasten method, transforms note-taking from storage into thinking. But which connected notes app is right for you?
What Makes Connected Notes Different
In a connected notes system:
- Notes link to notes : Create explicit relationships between ideas
- Backlinks appear automatically : See what links to the current note
- Knowledge compounds : Old notes gain value as you add new connections
- Discovery happens : Unexpected connections emerge from the network
- Graph visualization : See your knowledge visually
The goal isn't just storage:it's building a network that helps you think.
1. Obsidian : The Power User's Choice
Best for: Users who want maximum control and local-first storage
Obsidian stores everything as local Markdown files while providing powerful linking and visualization. Its plugin ecosystem enables almost any workflow.
Key features:
- Plain Markdown, fully portable
- Bidirectional links with backlinks panel
- Graph view showing note connections
- 1000+ community plugins
- Full customization with CSS/JS
- Local-first, you own your files
Pricing: Free for personal use, Sync $4/month, Publish $8/month
Pros:
- Complete control over your data
- Massive plugin ecosystem
- Active community
- No vendor lock-in
Cons:
- Significant learning curve
- Requires setup investment
- Mobile apps less polished
- No real-time collaboration
Best for: Technical users who want power, privacy, and portability.
2. Atlas : AI-Powered Connections
Best for: Users who want AI to discover connections automatically
Atlas takes a different approach: instead of manually creating links, AI discovers connections across your notes and documents. The knowledge graph emerges from content, not explicit linking.
Key features:
- AI-generated connections
- Knowledge graph visualization
- Chat with your entire knowledge base
- PDF and article support
- Natural language search
- Works immediately, no configuration
Pricing: Free tier available, Pro from $12/month
Pros:
- No manual linking required
- Discovers connections you'd miss
- Works with documents, not just notes
- Zero setup time
Cons:
- Cloud-based (no local storage)
- Less manual control over connections
- Newer tool, smaller community
- Different paradigm from traditional linking
Best for: Users who want connection benefits without manual linking work.
3. Roam Research : The Original Networked Notebook
Best for: Researchers and writers who think in blocks
Roam pioneered the modern connected notes movement. Its block-level references and daily notes workflow created a new paradigm for networked thought.
Key features:
- Block-level transclusion
- Daily notes as primary interface
- Bidirectional linking
- Queries and filters
- Real-time collaboration
- Academic-focused community
Pricing: $15/month or $165/year
Pros:
- Block references are powerful
- Strong for research and writing
- Real-time multiplayer
- Dedicated community
Cons:
- Expensive
- Web-only (no local backup)
- Development has slowed
- Interface feels dated
Best for: Serious researchers who value block-level connections.
4. Logseq : Open-Source Roam Alternative
Best for: Users who want Roam-like features with local storage
Logseq offers Roam's outliner approach with local storage and open-source development. It's the best free Roam alternative.
Key features:
- Outliner-based like Roam
- Local Markdown/org files
- Bidirectional links
- Built-in flashcards
- Queries and templates
- Active development
Pricing: Free (open source)
Pros:
- Free and open-source
- Local file storage
- Roam-like experience
- Active community
Cons:
- Requires outliner buy-in
- Less polished than Obsidian
- Sync needs third-party solution
- Steeper learning curve
Best for: Roam fans who want local storage and open source.
5. Notion : Connected Databases
Best for: Teams and users who want structured connections
Notion's "related databases" feature creates connections through structure rather than ad-hoc links. Notes connect through database relationships.
Key features:
- Database relations connect entries
- Templates ensure consistency
- Team collaboration built-in
- Notion AI for assistance
- Beautiful, polished interface
- Flexible organization
Pricing: Free for personal, Plus $10/month
Pros:
- Best team collaboration
- Structured connections
- Great onboarding
- Polished experience
Cons:
- No true bidirectional links
- Requires database design
- No knowledge graph
- Cloud-only
Best for: Teams who want connection through structure.
6. Capacities : Object-Based Connections
Best for: Visual thinkers who organize by "things"
Capacities organizes by objects:people, books, concepts:rather than documents. Objects naturally connect to each other, creating an intuitive network.
Key features:
- Object-based organization
- Automatic relationships
- Beautiful graph visualization
- Daily notes
- Media embedding
- Modern interface
Pricing: Free tier available, Pro from $9.99/month
Pros:
- Intuitive mental model
- Beautiful design
- Gentler learning curve
- Good mobile apps
Cons:
- Newer, smaller community
- Less extensible
- No local storage
- Still building features
Best for: Visual thinkers who prefer objects to documents.
7. Reflect : Networked Notes + AI
Best for: Users who want AI built into linked notes
Reflect combines Obsidian-like linking with built-in AI assistance. It feels modern and polished without requiring plugin management.
Key features:
- Bidirectional linking
- Built-in AI assistant
- End-to-end encryption
- Backlinks and graph view
- Calendar integration
- Clean, modern design
Pricing: From $10/month
Pros:
- AI native, not added on
- Excellent design
- Strong privacy (E2EE)
- Quick capture
Cons:
- No free tier
- Smaller ecosystem
- Less customizable
- Subscription required
Best for: Users who want polished AI + linking without DIY.
8. Apple Notes + iCloud : Surprisingly Connected
Best for: Apple users who want "good enough" linking
Apple Notes quietly added note linking. Combined with iCloud sync and Apple Intelligence, it's a surprisingly capable option for Apple users.
Key features:
- Basic note linking
- Apple Intelligence summaries
- Zero configuration
- Perfect Apple integration
- Quick capture from anywhere
- Completely free
Pricing: Free (with Apple devices)
Pros:
- Already installed
- Seamless ecosystem
- Apple Intelligence
- No learning curve
Cons:
- No backlinks
- No graph view
- Basic linking only
- Apple ecosystem only
Best for: Apple users who want simplicity over power.
Comparison Table
| App | Link Type | Graph View | AI | Local | Free | Collaboration |
|---|---|---|---|---|---|---|
| Obsidian | Manual | ✓ | Plugins | ✓ | ✓ | ✗ |
| Atlas | Auto | ✓ | Built-in | ✗ | ✓ | ✗ |
| Roam | Manual | ✓ | ✗ | ✗ | ✗ | ✓ |
| Logseq | Manual | ✓ | Plugins | ✓ | ✓ | ✗ |
| Notion | Databases | ✗ | Built-in | ✗ | ✓ | ✓ |
| Capacities | Objects | ✓ | Limited | ✗ | ✓ | ✗ |
| Reflect | Manual | ✓ | Built-in | ✗ | ✗ | ✗ |
| Apple Notes | Basic | ✗ | Built-in | Via iCloud | ✓ | Limited |
How to Choose
"I want maximum control and privacy" → Obsidian (local, extensible, yours forever)
"I don't want to manually link notes" → Atlas (AI creates connections automatically)
"I think in outlines and blocks" → Logseq (free) or Roam (premium)
"I need team collaboration" → Notion (databases) or Roam (real-time)
"I want beautiful with gentle learning" → Capacities (objects) or Reflect (AI)
"I just want simple linking" → Apple Notes (if Apple ecosystem)
Making Links Work For You
Having connected notes is one thing. Getting value from them is another. Here's how:
1. Link While Writing
Don't link after the fact. As you write, notice connections and create them immediately. If you're writing about "spaced repetition," link to your note on "memory techniques."
2. Develop Link Habits
- Concept links: Ideas that relate (memory → learning)
- Source links: Where ideas came from (papers, books)
- Project links: Relevant to what you're working on
- Question links: Things to explore further
3. Review Through Links
Instead of linear reading, follow links. Start with today's note, follow connections, discover forgotten ideas. Links enable non-linear exploration.
4. Trust the Graph
Even without perfect organization, linked notes create value. The graph view surfaces connections. Backlinks show relationships you forgot. The system works even imperfectly.
5. Let Connections Emerge
You don't need to know the "right" connection. Link what feels related. Patterns emerge over time. False connections get ignored; real ones get strengthened.
Connected Notes for Different Use Cases
Zettelkasten / PKM
Best tools: Obsidian, Logseq, Roam Focus: Atomic notes, permanent notes, emergent structure
Research
Best tools: Atlas, Obsidian + academic plugins, Roam Focus: Paper connections, concept development, synthesis
Writing / Creativity
Best tools: Roam (blocks), Obsidian (long-form), Atlas (synthesis) Focus: Draft connections, source tracking, idea development
Learning
Best tools: Logseq (flashcards), Obsidian, Capacities Focus: Concept links, review, knowledge building
Work / Projects
Best tools: Notion (team), Capacities (objects), Obsidian Focus: Project notes, meeting links, documentation
Frequently Asked Questions
What's the point of connected notes?
Connected notes help you think by making relationships explicit. Instead of notes existing in isolation, they form a network where ideas reinforce each other and unexpected connections emerge.
How many links should a note have?
There's no right number. Link what's genuinely related. Some notes naturally have many connections; others stand alone. Quality matters more than quantity.
Do I need a graph view?
The graph view is helpful for visualization but not essential. Many users rarely look at it. Backlinks (seeing what links to the current note) provide most of the value.
Can I use connected notes without the Zettelkasten method?
Yes. You don't need atomic notes or a complex system. Even basic linking adds value. Start simple and add structure only if you need it.
Which app has the best graph view?
Obsidian has the most customizable graph. Capacities has the most beautiful. Atlas generates graphs automatically. All are useful; none are essential.
What if I link wrong?
Links are cheap. Wrong links do no harm:you'll just ignore them. It's better to over-link than under-link. You can always remove connections later.