Markdown notes that stay encrypted on your own machine

A Markdown note is a plain-text note where a few punctuation marks do the formatting. A hash makes a heading, a hyphen makes a bullet, two asterisks make bold. That is why people move to Markdown: the file outlives the app. The part nobody mentions is that plain text is readable by anyone who reaches the folder. NotePrivate lets you write in the same syntax on Mac and Windows, keeps the vault encrypted with a key derived from your password, and exports every note back out as a plain .md file whenever you want.

macOS and Windows · You hold the keys · Export every note as Markdown, folders and attachments included

Definition

What a Markdown note actually is

Markdown is a way of writing formatting with normal keyboard characters, invented so a plain-text file could still look like a document. A Markdown note is just a note written that way.

Nothing is hidden in the file. There is no proprietary container, no database, no XML wrapper. Open it in Notepad or TextEdit thirty years from now and you can still read every word, which is the whole argument for taking notes this way. Here is what a real one looks like as raw text:

# Tuesday standup

## Blockers
- [ ] Waiting on the staging key
- [x] Reviewed the migration script

**Decision:** ship Thursday, not Wednesday.

See [[Release checklist]] and the [runbook](https://example.com).

That is a complete Markdown text example. Every mark in it is a character you already have on the keyboard, and a note-taking app that understands Markdown turns each one into real formatting as you type.

Why people switch to Markdown notes

  • The note is readable without the app that made it
  • Your hands never leave the keyboard for a toolbar
  • It diffs, greps and version controls like source code
  • Copy and paste keeps the structure, not a wall of soup

What Markdown does not give you

Privacy. A .md file is plain text by definition, so every word is legible to anything that can open the folder, including the sync client and the search indexer. NotePrivate is the part that fixes this, and the section below shows exactly how.

Syntax

How to write a note in Markdown

Full Markdown reference docs run to thousands of words because they cover documentation and web publishing. For notes you need about nine marks, and this is the list. Each row also says what the NotePrivate editor does with it.

You typeYou getIn NotePrivate
# TitleA headingFormats as you type the space. Levels 1 to 4
- itemA bullet listTab to indent a sub-bullet
1. itemA numbered listRenumbers itself when you reorder
- [ ] taskA checkboxA real tickable box. One level, not nested
**bold**Bold textYes, live as you close the asterisks
*italic*Italic textYes
BackticksInline codeYes, and three backticks open a code block
> quoteA blockquoteYes
[[Note title]]A link to another noteType two brackets and it suggests your titles

NotePrivate formats these inline rather than showing you a source pane beside a preview pane, so there is no split screen to manage. The syntax is what you type, not what you stare at.

The gap nobody writes about

A folder of .md files is a folder anyone can read

Every popular way of keeping Markdown notes stores them in the clear. That is the trade you are making, whether or not the app tells you.

The folder itself

Your notes sit in a directory as ordinary text. Anyone who borrows the unlocked laptop, restores the backup, or gets shell access reads the lot, and Spotlight or Windows Search has already indexed the contents for them.

The sync client

Dropbox, iCloud Drive or Google Drive uploads those .md files as plain text. The provider stores exactly what you wrote and can hand it to anyone with the legal paperwork.

The git repository

Keeping notes in git is a genuinely good system for history and portability. It also means every version of every note is stored in the clear, forever, and pushing to a remote publishes that archive to a server you do not control.

Disk encryption is the usual answer, and it is not one. FileVault and BitLocker protect a machine that is powered off. The moment you log in, the folder is decrypted for anything running as you. NotePrivate encrypts the vault itself with a master key that is wrapped by a key derived from your password, so the notes stay unreadable while the machine is on, and the password never leaves your device.

CapabilityNotePrivateA folder of plain .md files
Markdown syntax while you typeYesYes
Notes stay on your own diskYesYes
Works fully offlineYesYes
Unreadable on a logged-in machineYesNoPlain text to any process
Encrypted before it reaches your cloud folderYesNo
Password on a single noteYesNo
Attachments encrypted with the noteYesOn-device OCR for images and PDFsNo
Edit in any text editor on any machineNoExport firstYes
Plugins, themes and graph viewsNoYesVia Obsidian and similar
FreeNoNotePrivate is planned at $59/yearYes
Yes fullPartial limitedNo none

Details on other tools are a general reading and change over time; verify on the vendor's site.

The shortlist

Which Markdown notes app is best depends on what you are protecting

Roundups rank these on feature count. The more useful question is which trade you are willing to make, because every one of these apps makes a different one.

Obsidian

The default answer, and a good one. A folder of .md files you own, with plugins, backlinks and a graph view on top. The files are plain text on disk, and encryption means paid Sync or a plugin. The encrypted Obsidian alternative page goes through that gap in detail.

Bear

The nicest writing surface of the group if you are all-Apple, with Markdown that formats inline rather than in a split preview. It is a subscription for sync, Apple platforms only, and the notes are not encrypted with a key you hold.

Markdown plus git

A repository of .md files edited in VS Code or Vim. Free, portable, perfect history, and no vendor at all. The catch is that the history is a permanent plain-text archive, and you are now the person maintaining the setup.

Simplenote and Apple Notes

Simplenote is free and fast with a Markdown toggle. Apple Notes is already installed and takes some Markdown shortcuts, though it does not store notes as Markdown. Both keep your notes on the vendor's servers. See the Apple Notes alternative comparison.

Joplin and Standard Notes

The two free options that take encryption seriously. Joplin is end-to-end encrypted once you turn it on, and Standard Notes has an encrypted free tier with features split across paid plans. The Standard Notes alternative page covers where that split lands.

NotePrivate

For the person whose first requirement is that nobody else can read the notes. You write in Markdown, the vault is encrypted on your own disk on Mac and Windows, one flat planned price of $59 a year with every feature included, and the export is plain .md.

Details on other apps are a general reading and change over time; check the vendor's site before you decide.

Flavors

Which flavor of Markdown your notes should use

There is no single Markdown standard. The original spec left gaps, so different tools filled them differently, and that is why a note can look right in one app and wrong in another.

CommonMark is the strict specification most modern tools build on. GitHub Flavored Markdown adds tables, strikethrough, autolinked URLs and the checkbox syntax that note-takers actually care about. Obsidian layers wiki-style [[double bracket]] links on top, which are not in any spec but have become the convention for linking notes to each other.

For notes, stay inside the overlap. Headings, lists, bold, italic, code, quotes, links and checkboxes behave identically everywhere, and a note built from those marks survives every move you will ever make it do. The moment you reach for a flavor-specific extension, you have quietly tied the note to one app again, which was the thing Markdown was supposed to stop.

What NotePrivate speaks

  • Headings, levels 1 through 4
  • Bold, italic, strikethrough and inline code
  • Fenced code blocks with syntax highlighting
  • Bullet lists, numbered lists and blockquotes
  • GitHub-style checkboxes, one level deep
  • Links, plus [[title]] note links with autocomplete

Not supported: Markdown tables, headings below level four, and nested checkboxes. If your notes lean on tables, that is a real reason to pick something else.

Getting out

What a NotePrivate Markdown export looks like on disk

An encrypted vault is only acceptable if leaving is easy. Export all notes as Markdown writes a dated folder into your Downloads directory, and this is exactly what lands there.

NotePrivate Export 2026-08-16 143012/
  Work/
    Standups/
      Tuesday standup.md
    Q3 planning.md
    Q3 planning attachments/
      budget.pdf
  Personal/
    Reading list.md

One .md file per note, in a directory tree that mirrors the folders you built inside the vault. Nothing is bundled into a single archive file you then have to unpick.

Inside each file

  • The note title as a level-one heading
  • A Tags: line when the note has tags
  • The body, converted to Markdown from rich text if needed
  • An ## Attachments section linking each file by relative path

Attachments are written as real files in a sibling folder, so the links resolve when you drag the export into any other Markdown app. Notes carrying their own per-note password have to be unlocked before the export runs, which is the one step people forget.

Honest fit

When NotePrivate is the wrong Markdown notes app

You want to edit the raw files

NotePrivate is not a .md file editor pointed at a directory. The vault is encrypted, so you cannot open a note in Vim or pipe it through a script without exporting first. If editing the files directly is the point, Obsidian or a git repository is the honest answer.

You live in plugins and graph views

No plugin ecosystem, no community themes, no graph view, no Dataview queries. NotePrivate has folders, tags, saved searches and [[title]] backlinks, and that is the whole surface.

Your existing .md files must render on import

Importing .md files preserves the original characters exactly, so the Markdown marks arrive as visible text rather than being re-rendered as formatting. That is deliberate, because it guarantees nothing in your file is silently rewritten, but it is not what everyone expects.

You need free

NotePrivate is planned at $59 a year and is not on sale yet. If the budget is zero and you still want encrypted Markdown notes, Joplin and Standard Notes are the sensible stops, and a plain folder of .md files costs nothing at all.

FAQ

Questions, answered

What is a Markdown note?

A Markdown note is a note written in plain text where a few punctuation marks carry the formatting instead of a toolbar. A hash makes a heading, a hyphen makes a bullet, two asterisks make bold. The file stays readable even in an app that knows nothing about Markdown, which is why it outlives the app you wrote it in. NotePrivate lets you type that syntax and formats it live, then hands the note back as a plain .md file whenever you export.

How do I write a note in Markdown?

Start with a hash and a space for the title, then a hyphen and a space for each bullet. Two asterisks either side of a word make it bold, backticks make inline code, and a hyphen followed by empty square brackets makes a checkbox. That is roughly ninety percent of the syntax a note-taker ever uses. In NotePrivate you type those marks and the line formats as you go, so you never switch between a source pane and a preview pane.

What is a Markdown text example?

A short meeting note in Markdown looks like this: a line beginning with a hash for the title, a line beginning with two hashes for a section, hyphen-space lines for bullets, hyphen-space-brackets lines for checkboxes, two asterisks around a word to bold it, and square brackets followed by a URL in round brackets for a link. Every one of those marks is a normal keyboard character, so the note is still legible as raw text. There is a full example higher up this page.

Which Markdown notes app is the best?

It depends on what you are protecting. Obsidian is the strongest choice if you want plugins and a graph view over a folder of files you control. Bear is the nicest writing experience on Apple hardware. A folder of .md files in a git repository is free and the most portable option there is. NotePrivate is the one to look at if your first requirement is that nobody who picks up your laptop can read the notes, because it is the only one of those where the file on disk is ciphertext by default.

Are Markdown files encrypted?

No. A .md file is plain text by definition, so anyone who opens the folder can read it, and so can any backup, sync client or indexing service that touches it. Disk encryption like FileVault or BitLocker only protects a machine that is powered off. NotePrivate encrypts the vault itself with a master key wrapped by a key derived from your password, so the notes stay unreadable while the computer is running and logged in.

Can I import my existing Markdown files?

Yes. Point NotePrivate at your .md files and they import with their folder structure intact. They arrive as plain-text notes holding the original characters exactly as written, which means the Markdown marks stay visible as text rather than being re-rendered. That is deliberate, because it guarantees nothing in your file is silently rewritten on the way in. The same importer also reads Apple Notes, Evernote ENEX, Standard Notes backups, Google Keep and Simplenote JSON, HTML, DOCX, RTF and plain text.

Can I get my Markdown notes back out of NotePrivate?

Yes. Export all notes as Markdown writes a dated folder to your Downloads directory containing one .md file per note, in a directory tree that mirrors your folders. Each file opens with the note title as a heading, then a Tags line, then the body. Attachments are written to a sibling folder and linked from an Attachments section at the bottom of the file.

Which flavor of Markdown does NotePrivate use?

The common subset that every flavor agrees on, plus the checkbox syntax from GitHub Flavored Markdown. Headings, bold, italic, strikethrough, inline code, fenced code blocks, blockquotes, bullet and numbered lists, links and task lists all work. Tables are not supported in the NotePrivate editor, and headings stop at level four.

Does NotePrivate work offline?

Always. The vault lives on your Mac or PC and the app opens, searches and edits with no connection at all. Sync runs through a cloud folder you already own, still encrypted, and you can skip it entirely.

Can I keep a Markdown journal in NotePrivate?

Yes, and that is a common use. One folder per journal, one note per day, titled with the date so it sorts forever. The private journal app page walks through the setup, including auto-lock and per-entry passwords.

Own your notes. Starting today.

Private by design, rich enough to be your only notes app, and yours to keep forever.

macOS and Windows · End-to-end encrypted · Export anytime