Best Zettelkasten Software for 2025 (Full Showdown)

Do you want to start your digital Zettelkasten but don’t know which software to use?

That’s totally normal.

There are so many choices available that you can easily get bogged down. What if you choose the wrong app and then had to restart your Zettelkasten from scratch?

This comprehensive guide includes a complete list of Zettelkasten software to help you make the right choice.

I’m Matt Giaro, and I’m a note-taking maniac. I’ve helped hundreds of creators and thinkers set up their note-taking system to create online content using the Zettelkasten methodology.

💡 FREE RESOURCE: Don’t hesitate to check out my 7-DAY FREE EMAIL COURSE to help you start your digital Zettelkasten on the right foot:
👉 https://mattgiaro.com/signup-take-better-notes

Let’s dive into it.

📊 Quick Answer: Best Zettelkasten Apps at a Glance

If you’re in a hurry, here are my top picks for 2025:

  1. Obsidian – Free, cross-platform, local storage, markdown-based
  2. Logseq – Free, outliner-based, open source, graph view
  3. Roam Research – $15/month, web-based, powerful backlinking
  4. Mem.ai – Free tier available, AI-powered, clean interface
  5. Heptabase – Visual-first thinking, great for complex projects

Keep reading for detailed reviews, comparison tables, and expert recommendations for your specific use case.

📋 Contents

Chapter 1: What Makes a Good Zettelkasten App?
Chapter 2: Most Popular Zettelkasten Apps
Chapter 3: Best Free Zettelkasten Apps
Chapter 4: Best Zettelkasten Apps for Mac & iOS
Chapter 5: Best Zettelkasten Apps for Privacy
Chapter 6: Best Browser-Based Zettelkasten Apps
Chapter 7: Best Native Zettelkasten Apps
Chapter 8: Best for Android & Linux
Chapter 9: Best for Academics & Students
Chapter 10: Developer-Focused Solutions
Chapter 11: Complete App Comparison Table

🔥 Complete Zettelkasten Apps Comparison Table

Before we dive deep, here’s a comprehensive comparison to help you decide quickly:

AppPricePlatformsStorageGraph ViewMobileBest For
ObsidianFreeAllLocal/Markdown/Cloud✅ Yes✅ YesPower users, Privacy-focused
LogseqFreeAllLocal/Markdown/Cloud✅ Yes✅ YesOutliner lovers, FOSS fans
Roam Research$15/moWebCloud✅ Yes✅ YesCollaborative teams
NotionFree–$10/moAllCloud/Proprietary❌ No✅ YesProject management
Mem.aiFree–$15/moWeb, Mac, iOSCloud❌ No✅ iOSAI enthusiasts
Reflect$10/moMac, iOS, WebCloud/Encrypted❌ No✅ iOSApple users, Privacy
Heptabase$10/moMac, Win, WebCloud✅ Yes❌ NoVisual thinkers
CapacitiesFree–$10/moAllCloud✅ Yes✅ YesObject-based PKM
ZettlrFreeMac, Win, LinuxLocal/Markdown❌ No❌ NoAcademics with Zotero
Lattics$10/moMac, iOSCloud✅ Yes✅ YesBalanced features
SupernotesFree–$10/moAllCloud❌ Limited✅ YesCard-based notes
CraftFree–$12/moMac, iOS, WebCloud❌ No✅ YesBeautiful design

Key Takeaways:

  • ✅ For beginners: Start with Obsidian or Logseq (both free)
  • ✅ For privacy: Obsidian or Logseq (local storage)
  • ✅ For academics: Zettlr (Zotero integration) or Obsidian
  • ✅ For AI features: Mem.ai or Capacities
  • ✅ For visual thinkers: Heptabase or Obsidian (with Canvas)

Chapter 1: What Makes a Good Zettelkasten App?

Before digging deeper into which app you should choose, let’s define the criteria that make a good Zettelkasten app.

Bidirectional Linking

One of the main reasons people start a Zettelkasten is to link notes together.

It blows my mind how many people try to create their digital slip box with an app that’s not designed to work with backlinks out of the box. Great examples are Apple Notes or Evernote as a Zettelkasten.

Now, when you take the time to look at how these apps actually work, you see that they have a link-sharing feature. But this feature takes way too many clicks. Plus, it doesn’t give you a clear overview of all links pointing from or to a specific note.

If you’re serious about building a Zettelkasten, you need to pick an app that supports backlinking out of the box. And not stupid workarounds.

Graph View (or a Way to See What Notes Are Linked)

The graph view is an essential part of my Zettelkasten workflow.

The reason? Simple.

Because it gives you a visual representation of how your notes are connected together. Especially if you’re a visual thinker, this feature is a must-have.

Some apps allow you to create backlinks out of the box but lack a graph view feature.

This is why I don’t recommend using Bear as a Zettelkasten, for example. Bear is the prettiest app I have come across over the years, and I still use it daily.

But for the Zettelkasten? No thanks. There is a way to link notes together, but I have absolutely no visibility on how they’re connected.

Use a Zettelkasten software that has a graph view.

Speed

It may not seem like a big deal, but Speed is extremely important when taking notes.

Here’s why: When you have an idea, you want to jot it down as quickly as possible.

You also want to navigate within your Zettelkasten blazing fast so that you can find the best connections between your atomic notes.

A slow digital slip box app will slow down your workflow and kill the joy and excitement of discovering your best ideas.

You’ll probably end up frustrated and abandon your system.

I’m a strong believer that UI and UX are one of the most essential parts of software development. (This is also why you see me frequently rant about stupidly designed apps…)

Speed matters when it comes to picking your Zettelkasten app.

You want an app:

  • That launches quickly
  • That allows you to edit your notes
  • And gives you the freedom to navigate between your notes

As fast as possible!

Don’t let a tortoise-like Zettelkasten app slow down your thinking!

Future-Proof & Data Portability

We live in a fast-changing environment.

And just because an app exists today, doesn’t mean it will be here tomorrow. If you’re serious about taking notes, then you certainly want to build a network of notes that will last for years to come. This is where the future-proof criteria come into play.

You want the format your notes are being saved in to be as future-proof as possible. This means that you don’t want to get locked into a proprietary system that you can only hardly switch from.

Here’s what you should look for:

✅ Plain Text & Markdown Formats

I’m a big advocate of plain text – written in Markdown – because it’s lightweight and data-portable.

Think about it: You can open a .txt or .md file with ANY text editor, on ANY device, from ANY decade. Try opening a Word document from 1995… not fun.

Apps that use plain text/Markdown:

  • Obsidian ✅
  • Logseq ✅
  • Zettlr ✅
  • Vim-Zettel ✅

Apps with proprietary formats:

  • Notion ⚠️ (proprietary database)
  • Roam Research ⚠️ (can export to Markdown)
  • Mem.ai ⚠️ (limited export)

⚠️ Warning: Vendor Lock-In

You do not want to get locked into a notes app and several years down the road find it has gotten so bloated and slow it’s unusable.

Or worse – the company goes bankrupt and you lose access to years of work.

The notes in your Zettelkasten belong to you, not to the software you’re using.

A red flag should be raised when you see a Zettelkasten app that does not allow you to export your notes in a widely-accepted and friendly format like plain text or markdown files.

Make your Zettelkasten future-proof by choosing the right software.

Syncing Your Zettelkasten

Most people want to access their Zettelkasten from anywhere.

This is when cloud sync comes into play.

Your Zettelkasten app should ideally have a sync feature.

Options:

  • Built-in sync: Roam, Notion, Mem.ai, Craft
  • Optional paid sync: Obsidian Sync ($10/mo), Logseq Sync (coming soon)
  • Third-party sync: Use iCloud, Dropbox, or Google Drive with local-first apps

Privacy

Some people may store sensitive information in their Zettelkasten app. If that’s you, you should look for how your data is handled and opt for end-to-end encryption (or simply store your notes locally).

Cross-Platform

The type of device you use will definitely influence how you pick the right Zettelkasten app. A person who uses only Apple devices will not have the same choices as someone who uses both Apple and Windows devices.

This is why you have to be clear about the types of devices you plan to use to access your Zettelkasten.

Exporting Your Notes

This criterion is strongly related to the future-proofing of your notes.

The notes in your Zettelkasten belong to you, not to the software you’re using.

A red flag should be raised when you see a Zettelkasten app that does not allow you to export your notes in a widely-accepted and friendly format like plain text or markdown files.

Chapter 2: Most Popular Zettelkasten Apps

How to measure popularity? The yardstick I used was simply checking how many people talk about the following Zettelkasten apps.

So here’s what I found:

🥇 #1: Obsidian

Obsidian has over 70,000 members on their Discord channel and 35,000 members on their forum (Source)

Why it’s popular:

  • ✅ Completely free (optional paid sync)
  • ✅ Local-first, markdown files
  • ✅ Massive plugin ecosystem
  • ✅ Works offline
  • ✅ Privacy-focused

Pricing: Free (Sync: $10/mo, Publish: $20/mo)

Best for: Privacy-conscious users, developers, power users

🥈 #2: Roam Research

Roam Research was probably the first mainstream bi-directional linking app. Big YouTubers like Ali Abdaal or productivity nerds like Nat Eliason have been talking about Roam quite extensively. And it seems that Roam still has a great market share thanks to that.

Why it’s popular:

  • ✅ First mover advantage
  • ✅ Powerful block-level references
  • ✅ Strong community
  • ✅ Regular updates

Pricing: $15/month or $165/year

Best for: Power users who want web-based access

🥉 #3: Notion

Finally, Notion. Let me be clear: Notion is NOT a Zettelkasten app. Yes, it allows you to link your notes. Yes, it allows you to see backlinks with some workarounds, but… Notion is first and foremost a collaboration tool.

I still had to include it here because so many people still use Notion as their slip-box (and this is why most of their workflow is broken). Since in this section my yardstick is popularity, ranking Notion as #3 made sense.

Pricing: Free for personal use, $10/mo for teams

Best for: Project management and collaboration (but not pure Zettelkasten)

Chapter 3: Best Free Zettelkasten Apps

Okay, you want to start taking notes using the Zettelkasten methodology but don’t want to pay a dime?

Here are the best free Zettelkasten apps for 2025:

🥇 #1: Obsidian

Obsidian is free. You only have to pay for it if you want advanced features like Sync or Publish. You could also donate to support the project. It’s the best free Zettelkasten app in 2025.

Pros:

  • ✅ Completely free for personal use
  • ✅ Local storage (your data, your control)
  • ✅ Markdown files (future-proof)
  • ✅ Graph view included
  • ✅ Huge plugin ecosystem (Canvas, Daily Notes, etc.)
  • ✅ Works offline

Cons:

  • ❌ Steeper learning curve
  • ❌ Mobile app could be better
  • ❌ Sync costs extra ($10/mo)

Official site: obsidian.md

🥈 #2: Logseq

Logseq is free, too. The main difference between Obsidian and Logseq is that Logseq uses bullets like Roam, while Obsidian is more geared towards a normal text editor. Logseq has a growing community, and I wouldn’t be surprised if Logseq outbeats Obsidian in terms of popularity in the upcoming years.

Pros:

  • ✅ 100% free and open source
  • ✅ Outliner-based (great for bullet journaling)
  • ✅ Local-first, markdown files
  • ✅ Graph view included
  • ✅ Active development

Cons:

  • ❌ Outliner format not for everyone
  • ❌ Less plugin ecosystem than Obsidian
  • ❌ Mobile app still maturing

Official site: logseq.com

🥉 #3: Mem.ai (Free Tier)

Mem.ai is an interesting solution but works only in the browser (or on the Apple ecosystem). Their free plan allows you to store an unlimited amount of notes, add up to 25 MB file size per upload for a total of 5 GB storage (which is way more than enough).

Pros:

  • ✅ Free tier with unlimited notes
  • ✅ AI-powered features
  • ✅ Clean, modern interface
  • ✅ Fast and lightweight

Cons:

  • ❌ Apple-only for native apps
  • ❌ Cloud-only (no local storage)
  • ❌ Limited export options

Official site: mem.ai

Honorable Mentions (Free)

Zettlr – Free and open source, perfect for academics who need Zotero integration.
Capacities – Free tier available, object-based PKM with AI features.
Kortex – Emerging free option with solid features.

Chapter 4: Best Zettelkasten Apps for macOS and iOS

Apple users are design maniacs.

They love smooth and fast interfaces.

So in this section I exclusively cherry-picked Zettelkasten apps who had a native Desktop and Mobile app for Apple devices.

🥇 #1: Obsidian

Honestly speaking, I wasn’t going to rank Obsidian in this section. Why? Because their interface stinks, especially on mobile. But Obsidian improved a lot their iOS app since version 1.0. And since there’s so much you can do with Obsidian, I had to rank it first.

Apple-specific features:

  • ✅ Native Mac & iOS apps
  • ✅ Works with iCloud sync (free alternative to Obsidian Sync)
  • ✅ iOS Share Sheet integration
  • ✅ Keyboard shortcuts support

Pricing: Free

🥈 #2: Mem.ai

Mem is definitely an app that starts getting a lot of traction. It has great native apps for iPhone and Mac.

Apple-specific features:

  • ✅ Beautiful native Mac app
  • ✅ Fast iOS app
  • ✅ Spotlight search integration
  • ✅ AI-powered smart search

Pricing: Free tier, $15/mo Pro

🥉 #3: Reflect

Finally, Reflect seems interesting, too. Plus, they have native Kindle highlight syncing which removes a lot of friction. Yet, they make it hard to switch since they don’t have markdown file import support. If you want to start using Reflect, you have to start your notes from scratch.

Apple-specific features:

  • ✅ Beautiful native apps
  • ✅ Calendar integration
  • ✅ Kindle highlights sync
  • ✅ End-to-end encryption

Pricing: $10/month

Official site: reflect.app

Worth Considering:

Logseq – Recently launched their mobile app, too. Competition here is tough.

Craft – Certainly the best app out there for Mac & iOS when it comes to design. Not to mention their iOS Shortcuts integration to make powerful capturing automations. The only thing that bothers me with Craft is that there is no graph view.

Lattics – Featured in YouTube videos as the “(almost) perfect note app” with excellent Apple ecosystem integration.

Chapter 5: Best Zettelkasten Apps for Privacy

Privacy matters.

And this is why you may be looking for a Zettelkasten app that’s Privacy friendly.

When it comes to privacy, probably nothing trumps being able to store your data locally.

Here are the best privacy-focused Zettelkasten apps:

🥇 #1: Obsidian (Local Storage)

Obsidian offers you the ability to store your notes locally.

And… it works on every platform.

Privacy features:

  • ✅ 100% local storage
  • ✅ No cloud required
  • ✅ Your files, your control
  • ✅ Optional E2E encrypted sync

Obsidian Sync (optional, $10/mo) states that their Sync option is end-to-end encrypted and that they don’t have access to your encryption keys, which makes it an option to consider to ally between a local and cloud-based encrypted Zettelkasten.

🥈 #2: Logseq (Local Storage)

Logseq also offers you the ability to store your notes locally.

Privacy features:

  • ✅ 100% local storage
  • ✅ Open source (auditable)
  • ✅ No tracking
  • ✅ Works offline

🥉 #3: Reflect (End-to-End Encrypted)

Reflect is one of few note-taking apps that supports end-to-end encryption. Keep in mind that Reflect only works on the Apple ecosystem.

Privacy features:

  • ✅ End-to-end encryption
  • ✅ Zero-knowledge architecture
  • ✅ Cannot be accessed by Reflect team
  • ✅ GDPR compliant

Chapter 6: Best Browser-Based Zettelkasten Apps

Maybe you’re the type of person who doesn’t care about native apps, but prefers being able to access your Zettelkasten via the browser.

If that’s you, here are the best alternatives to running a browser-based Zettelkasten:

🥇 #1: Supernotes

Supernotes has a fast, accessible browser interface.

Why Supernotes:

  • ✅ Blazing fast web app
  • ✅ Card-based interface
  • ✅ Real-time collaboration
  • ✅ Works offline (PWA)

Pricing: Free tier, $10/mo Pro

Official site: supernotes.app

🥈 #2: Craft

Craft launched their browser app in public beta in August 2022.

Why Craft:

  • ✅ Beautiful interface
  • ✅ Great for documents
  • ✅ Collaboration features
  • ✅ Template library

Pricing: Free tier, $12/mo Pro

🥉 #3: Roam Research

Roam, the OG, has always been accessible via browser only. (They recently launched their mobile app, but the feedback ain’t great).

Why Roam:

  • ✅ Powerful block references
  • ✅ Fast search
  • ✅ Mature feature set
  • ✅ Strong community

Pricing: $15/month

Chapter 7: Best Native Zettelkasten Apps

If you have devices running on multiple Operating Systems and would like to keep the benefits of native-first interfaces, this section is for you.

In order to qualify for this section, the requisites were simple: having an Android and iOS app and a desktop app for macOS and Windows.

Here are the best native and cross-platform Zettelkasten apps for 2025:

🥇 #1: Obsidian

Obsidian, once again, ranks first. Their mobile experience has vastly improved since v 1.0. The thriving community, their future-proof markdown files, and their $0 price-tag simply make it a no-brainer.

Cross-platform support:

  • ✅ Windows, Mac, Linux
  • ✅ iOS & Android
  • ✅ All features on all platforms

🥈 #2: Supernotes

Supernotes is a newcomer but rises quickly. The user interface is interesting, and offers everything you need to create a great Zettelkasten on every device. However, I’d like to see the character limit for notes removed.

Cross-platform support:

  • ✅ Web, Windows, Mac, Linux
  • ✅ iOS & Android
  • ✅ PWA support

🥉 #3: Logseq

Logseq is growing fast, and if you like creating bullet-point oriented notes, you may want to have a look at this Workflowy-style app to build your zettelkasten.

Cross-platform support:

  • ✅ Windows, Mac, Linux
  • ✅ iOS & Android
  • ✅ Open source

Chapter 8: Best Zettelkasten Apps for Android & Linux

Let’s face it: Most note-taking apps are built for Apple users first.

But if you’re on Android or Linux, you need apps that treat you as a first-class citizen.

Best for Android:

🥇 Obsidian

  • Native Android app
  • Full feature parity with desktop
  • Sync via Google Drive or Obsidian Sync
  • Works offline

🥈 Logseq

  • Native Android app
  • Open source
  • Local storage
  • Graph view on mobile

🥉 Capacities

  • Beautiful Android app
  • Object-based notes
  • AI features
  • Cloud sync

Best for Linux:

🥇 Obsidian

  • .deb, .AppImage, Snap packages
  • Full desktop features
  • Community support

🥈 Logseq

  • Native Linux support
  • Open source
  • Active Linux community

🥉 Zettlr

  • Built specifically for Linux users
  • Lightweight
  • Zotero integration
  • Free and open source

Official site: zettlr.com

Chapter 9: Best Zettelkasten Apps for Academics & Students

If you’re a researcher, PhD student, or academic, you need more than just note-taking. You need reference management, citation tools, and PDF annotation.

🥇 #1: Zettlr (Best for Zotero Integration)

Zettlr is built specifically for academics who use Zotero or JabRef.

Academic features:

  • ✅ Native Zotero integration
  • ✅ JabRef support
  • ✅ Citation management
  • ✅ Export to LaTeX
  • ✅ Free and open source

Pricing: Free

Official site: zettlr.com

🥈 #2: Obsidian (with Plugins)

Obsidian has a thriving academic community with powerful plugins.

Academic plugins:

  • ✅ Zotero Integration plugin
  • ✅ Citations plugin
  • ✅ Pandoc integration
  • ✅ PDF annotation plugins

🥉 #3: Capacities

Capacities is gaining traction in academic circles for its object-based approach.

Academic features:

  • ✅ Tag papers as objects
  • ✅ Link authors, concepts, papers
  • ✅ AI-powered insights
  • ✅ Clean interface

Pricing: Free tier, $10/mo Pro

Official site: capacities.io

Essential Integrations for Academics:

Reference Managers:

  • Zotero (free, open source)
  • Mendeley
  • JabRef

Reading Tools:

  • Readwise (highlights from papers)
  • LiquidText (PDF annotation)
  • MarginNote (visual learning)

Workflow Example for PhD Students:

  1. Reading: Use Zotero + PDF reader
  2. Highlights: Export to Readwise
  3. Notes: Process in Obsidian/Zettlr
  4. Links: Connect concepts in your Zettelkasten
  5. Writing: Export to LaTeX or Pandoc

Chapter 10: Best Zettelkasten Apps for Developers

If you’re a developer, you probably want to use your existing tools. Or at least something that fits your workflow.

🥇 #1: Obsidian

Obsidian is beloved by developers for good reasons.

Developer features:

  • ✅ Markdown + code blocks
  • ✅ Git version control
  • ✅ Plugin API (JavaScript)
  • ✅ Vim keybindings
  • ✅ Command palette

🥈 #2: Vim-Zettel

Vim-Zettel is a Vim plugin for Zettelkasten.

Why Vim users love it:

  • ✅ Never leave Vim
  • ✅ Plain text files
  • ✅ Fast navigation
  • ✅ Customizable

How to get started:

Plug 'vimwiki/vimwiki'
Plug 'michal-h21/vim-zettel'

Official: github.com/michal-h21/vim-zettel

🥉 #3: VS Code Extensions

VS Code users can turn their code editor into a Zettelkasten.

Recommended extensions:

  • Foam (Zettelkasten in VS Code)
  • Markdown Notes
  • Markdown Links

How to get started:

  • Install Foam extension
  • Use markdown files
  • Link with [[wiki-links]]

Other Developer Options:

Emacs Org-roam:

  • For Emacs users
  • Org-mode based
  • Extremely powerful
  • Steep learning curve

Neuron:

  • Static site generator
  • Plain text Zettelkasten
  • Deploy to web
  • Command-line based

Chapter 11: Modern Apps with AI-Powered Features

AI is changing how we take notes. Here are apps leading the charge:

Mem.ai (Best AI Features)

AI capabilities:

  • ✅ Smart search
  • ✅ Auto-tagging
  • ✅ Similar notes suggestions
  • ✅ AI-powered connections

Pricing: Free tier, $15/mo Pro

Capacities

AI capabilities:

  • ✅ AI assistant
  • ✅ Smart connections
  • ✅ Content generation
  • ✅ Object recognition

Pricing: Free tier, $10/mo Pro

Obsidian (AI Plugins)

AI plugins:

  • Smart Connections
  • Text Generator
  • Copilot
  • Ava (AI assistant)

New & Emerging Apps Worth Watching

Heptabase – Visual-First Thinking

Heptabase is gaining massive traction for its visual approach.

Why it’s special:

  • ✅ Visual whiteboard interface
  • ✅ Card-based notes
  • ✅ Great for complex projects
  • ✅ Tag system
  • ✅ Cross-platform

Best for: Visual thinkers, researchers working on complex topics

Pricing: $10/month

Official site: heptabase.com

Lattics – Almost Perfect

Lattics is featured in YouTube videos as the “(almost) perfect note app.”

Why it’s interesting:

  • ✅ Balanced feature set
  • ✅ Clean interface
  • ✅ Good mobile apps
  • ✅ Regular updates

Pricing: $10/month

Kortex (by Eden)

Kortex is a new player with solid fundamentals.

Features:

  • ✅ Backlinking
  • ✅ Graph view
  • ✅ Local storage option
  • ✅ Free tier

🎯 How to Choose: Decision Framework

Still not sure? Here’s my framework:

Choose Obsidian if you:

  • Want local storage and privacy
  • Like customization and plugins
  • Don’t mind a learning curve
  • Want free forever

Choose Logseq if you:

  • Love outliner-style notes
  • Want open source
  • Like bullet journaling
  • Want free forever

Choose Roam Research if you:

  • Need web-based access
  • Want mature, stable software
  • Don’t mind subscription
  • Value strong community

Choose Mem.ai if you:

  • Want AI-powered features
  • Use Apple devices
  • Like clean, simple interfaces
  • Want fast capture

Choose Zettlr if you:

  • Are an academic
  • Use Zotero or JabRef
  • Write in LaTeX
  • Want free software

Choose Heptabase if you:

  • Think visually
  • Work on complex projects
  • Like whiteboard-style notes
  • Don’t need mobile urgently

Choose Capacities if you:

  • Want object-based PKM
  • Like AI features
  • Need mobile apps
  • Want modern interface

Integration & Ecosystem

Your Zettelkasten doesn’t exist in isolation. Here’s how to build a complete knowledge workflow:

Reference Management:

  • Zotero (free, open source) → Works with Zettlr, Obsidian
  • JabRef → Works with Zettlr
  • Mendeley → Export to BibTeX

Reading & Highlights:

  • Readwise → Syncs highlights to most apps
  • LiquidText → PDF annotation
  • Kindle → Export highlights
  • Instapaper → Article highlights

Capture Tools:

  • Drafts (iOS) → Quick capture to Obsidian
  • Shortcuts (iOS) → Automation
  • Zapier → Connect web apps
  • IFTTT → Automation

Publishing:

  • Obsidian Publish → Publish notes to web
  • Quartz → Free alternative to Publish
  • Jekyll → Static site from markdown

Common Mistakes to Avoid

1. App Hopping

Don’t switch apps every month. Pick one and commit for at least 6 months.

2. Over-Organizing

Don’t spend more time organizing than creating. Your Zettelkasten should help you think, not become a filing cabinet.

3. Ignoring Data Portability

Choose apps with good export. Future you will thank you.

4. Not Using Plain Text

Proprietary formats are a trap. Stick with markdown when possible.

5. Chasing Features

You don’t need every feature. Pick what matches your workflow.

Final Verdict: My Personal Rankings

After years of testing, here’s what I recommend:

🥇 Overall Best: Obsidian

  • Free, private, future-proof, extensible

🥈 Best Free Alternative: Logseq

  • Open source, outliner-based, growing fast

🥉 Best for Beginners: Mem.ai

  • Simple, clean, AI-powered

🏆 Best for Academics: Zettlr

  • Built for research workflows

🏆 Best for Visual Thinkers: Heptabase

  • Whiteboard-based, intuitive

🏆 Best for Developers: Obsidian or Vim-Zettel

  • Git integration, plain text, extensible

🏆 Best for Apple Users: Reflect or Lattics

  • Native apps, beautiful design

Frequently Asked Questions

Can I use Notion for Zettelkasten?

Technically yes, but I don’t recommend it. Notion is built for project management, not interconnected thinking. The backlinks feature is clunky and there’s no graph view.

What about Evernote?

Evernote is not built for Zettelkasten. It’s a web clipper and document storage tool, not a thinking environment.

Do I need paid features?

No! Obsidian and Logseq are completely free. You only need paid features if you want official sync or publishing.

What if the app shuts down?

This is why plain text matters. If you use Obsidian, Logseq, or Zettlr, your notes are just markdown files. You can open them in any text editor forever.

How do I migrate between apps?

Most apps let you export to markdown. Obsidian and Logseq can directly read each other’s files since they both use markdown.

Take Action: Start Your Zettelkasten Today

Don’t overthink it. Here’s what to do:

For Beginners:

  1. Download Obsidian (free)
  2. Create your first note
  3. Create a second note and link to the first
  4. Keep going

For Academics:

  1. Set up Zotero (reference manager)
  2. Download Zettlr
  3. Connect Zotero to Zettlr
  4. Start processing papers

For Developers:

  1. Download Obsidian
  2. Initialize a Git repo in your vault
  3. Install community plugins
  4. Start documenting what you learn

For Visual Thinkers:

  1. Try Heptabase (7-day trial)
  2. Create your first whiteboard
  3. Add cards and connections
  4. See if it clicks

ENJOYED THIS GUIDE?

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Conclusion

Choosing a Zettelkasten app is less about features and more about what fits your workflow.

My recommendation:

Start with Obsidian or Logseq (both free, both use plain text).

Try them for 30 days. If one doesn’t fit, try the other.

Don’t overcomplicate it. The best Zettelkasten is the one you’ll actually use.

Now stop reading and start writing. Your future self will thank you.

— Matt Giaro

Last updated: October 2025