Two philosophies dominate this category: zero-knowledge cloud sync
(Standard Notes, Notesnook, Cryptee) where your notes are encrypted
before they ever leave your device, and local-first plain-text tools
(Joplin, Logseq, Zettlr) that store Markdown files you control and
sync however you like—Syncthing, your own server, or nothing at all.
Neither approach is strictly better. Cloud sync is more convenient
across devices; local-first gives you a file format that will still
open in a plain text editor in twenty years, encrypted or not.
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Standard Notes encrypts every note end-to-end by default and
backs that claim with four published third-party security audits
going back to 2017 (Cure53 twice, Trail of Bits, Shackle
Labs)—more than any other app in this category. It ships on
every major platform, supports extensions for Markdown, rich
text, spreadsheets, and code, and makes a public ten-year
longevity pledge for the project itself.
Pros
Four published third-party audits, more than any
competitor here
10-year longevity pledge
Self-hostable sync server
Encryption on by default, no configuration
Cons
Free tier is plaintext-only; encryption features are
behind a paid tier
Paid plan (~$90/yr) costs more than most alternatives
Editor extensions add a small learning curve
Ideal for: Readers who weigh independent audit
history heavily when trusting a vault with sensitive notes.
Pricing: Free plaintext tier; Productivity plan
(encryption, extensions) around $90/yr.
Platforms: Web, Windows, macOS, Linux, Android,
iOS.
Why it's here: The pick when you want the most
independently verified encryption claims in this category.
Notesnook applies the same zero-knowledge, end-to-end encryption
model as Standard Notes but keeps encryption on the free tier
and undercuts it heavily on price—its cheapest paid tier runs a
fraction of Standard Notes' annual cost. It's open source and
self-hostable, with a more modern notebooks-and-tags editor,
though it hasn't published a third-party security audit the way
Standard Notes has.
Pros
Encryption included free, not paywalled
Cheapest paid tier in this category
Modern editor with notebooks, tags, and rich formatting
Open source and self-hostable
Cons
No published third-party security audit (the company says
so itself)
Smaller ecosystem and community than Standard Notes
No real-time collaboration features
Ideal for: Budget-conscious readers who want
zero-knowledge encryption without paying for it.
Pricing: Free tier with real encryption;
Essential from about $2/mo, Pro from about $7/mo (annual pricing
lower). Platforms: Web, Windows, macOS, Linux,
Android, iOS.
Why it's here: The value pick—same encryption
promise as pricier competitors, without the audit trail to
match.
Joplin stores notes as plain Markdown files and offers optional
end-to-end encryption on top, syncing through Nextcloud, WebDAV,
Dropbox, or a local folder you manage yourself (Syncthing, a USB
drive, whatever you trust). Nothing is locked to a vendor's
cloud, which makes it the safest long-term bet against any
single company disappearing.
Pros
Free and fully open source
Encryption is optional but available on any sync backend
Plain Markdown files—readable in any text editor, forever
Sync backend is entirely your choice
Cons
Encryption is opt-in, not on by default
UI is less polished than Standard Notes or Notesnook
No official hosted sync service—you provide the backend
Ideal for: Readers who want maximum format
longevity and don't want to depend on any vendor's sync
infrastructure.
Cryptee bundles encrypted documents, notes, and photo storage
into one client-side-encrypted suite, built with a particular
focus on people who need strong privacy protections such as
journalists and survivors of abuse. Documents support Markdown
and math notation, and everything is encrypted before it leaves
the device—closer in scope to a small encrypted Google
Docs/Photos than a pure note app.
Pros
Combines notes, documents, and encrypted photo storage
Client-side encryption on everything, including images
Built with a specific focus on high-risk users
Cons
Smaller company and community than the bigger names here
Free tier storage is modest
Not a fit if you only want plain-text notes with no
photo/doc features
Ideal for: Readers who want notes, documents,
and private photo storage under one encrypted account.
Pricing: Free tier with limited storage; paid
plans add storage and features. Platforms: Web
(installable as a PWA on desktop and mobile).
Why it's here: The pick when you want more than
notes—documents and photos encrypted the same way.
Logseq is an open-source outliner for knowledge management,
storing everything locally in plain Markdown or Org-mode files
with bidirectional linking, PDF annotation, and task management.
A newer database version adds SQLite-backed graphs with optional
real-time sync, but the core promise—your data lives in files
you own—hasn't changed.
Pros
Local-first, plain-text file storage
Bidirectional linking and outliner workflow
Growing plugin ecosystem
Free and open source
Cons
Steeper learning curve than a simple notes app
Encryption depends on your storage/sync choice, not
built-in by default
Best suited to networked note-taking, overkill for simple
journaling
Ideal for: Readers building a linked knowledge
base (Zettelkasten-style) rather than simple flat notes.
Pricing: Free, open source.
Platforms: Windows, macOS, Linux desktop apps;
web version; mobile app for iOS.
Why it's here: Rounds out the list for power
users who want linked notes, not just a list of documents.
Zettlr is an open-source Markdown editor aimed at academics and
writers, with citation manager integration (Zotero, JabRef),
Pandoc/LaTeX export, and Zettelkasten-style knowledge
management. Like Joplin and Logseq, files stay local and in your
control; Zettlr's edge is export quality for people who need to
turn notes into publishable documents.
Pros
Local Markdown files you fully control
Strong citation and academic export tooling (Pandoc,
LaTeX)
Free and open source
Available in over a dozen languages
Cons
No built-in sync or encryption—bring your own
Feature depth aimed at academic writing, less useful for
casual notes
Smaller general-audience community than Joplin
Ideal for: Academics and researchers who need
Zettelkasten-style notes plus serious export tooling.
Pricing: Free, open source.
Platforms: Windows, macOS, Linux.
Why it's here: The specialist pick for research
and academic writing workflows.
An unpublished audit isn't proof of a flaw.
Notesnook's encryption is real and reviewable as open source—it
simply hasn't paid for the formal third-party audit Standard Notes
has. Weigh that honestly rather than assuming the worst.
Local-first means you own backups too. Joplin,
Logseq, and Zettlr won't lose your notes to a company shutting
down, but they also won't back them up for you unless you set that
up yourself.
Recovery keys are non-negotiable. Every
zero-knowledge app here means a lost password is unrecoverable by
design. Store recovery codes in your password manager, not a
sticky note.
Which is safer: cloud-encrypted notes or local Markdown files?
Both can be safe. Cloud-encrypted apps protect you if the
provider is breached or subpoenaed; local files protect you
from a company disappearing entirely. Pick based on which
failure mode worries you more.
Should I store passwords in a notes app?
No—use a dedicated password manager (see our password managers
guide). Even encrypted notes apps aren't built for the
autofill, breach monitoring, and structured secrets a password
manager provides.
Can I move between these apps later?
Markdown-based tools (Joplin, Logseq, Zettlr) export cleanly
since that's their native format. Zero-knowledge apps like
Standard Notes and Notesnook support export too, but check the
current export format before committing years of notes to one
vendor.
