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Apple Notes Exporter Pro · Troubleshooting

Apple Notes Export Folder Structure Not Preserved? Here Are 4 Fixes

Bulk-export from Apple Notes and every file lands in one flat folder, no matter how you organized them. Here is exactly why, and four ways to keep your folders intact, from free workarounds to a dedicated tool.

By Ram Velmurugan · Founder & Lead Developer, 1dot.ai

Verified against Apple's own documentation, Sept 2026·8 min read
Quick answer: Apple Notes' native bulk export (File > Export as > Markdown or PDF) does not preserve folder structure. Every note you select, regardless of which Notes folder it came from, lands as an individual file in the one destination folder you choose. Apple's own support documentation only offers a “Preserve folder structure on import” option; there is no equivalent for export. The fix is either exporting folder by folder manually, using a free open-source tool that recreates the structure automatically, or a dedicated exporter like Apple Notes Exporter Pro.

Editorial note: 1dot.ai makes Apple Notes Exporter Pro, one of the four options compared below. Every claim about Apple's native export is sourced to Apple's own support documentation and verified live at the time of writing. The free options are described honestly, including where they are genuinely a better fit than our own product.

macOS 26 Tahoe gave Apple Notes a real, built-in Markdown export for the first time, and it is a genuine improvement over the old one-note-at-a-time PDF export. We covered what it does well and where it falls short back in August, and one gap flagged there deserves its own guide: what actually happens to your folders when you export more than a note or two, and what to do about it.

If you organize your notes into folders like Work, Personal, or Recipes, you need to know this before you run a big export, not after you go looking for a note and find a pile of unsorted files instead.

Table of Contents
  1. What Apple Actually Documents
  2. What a Flattened Export Actually Looks Like
  3. Why Import Gets This Feature and Export Doesn't
  4. Fix 1: Export One Folder at a Time (Free, Manual)
  5. Fix 2: A Free Open-Source Tool That Automates It
  6. Fix 3: DIY with an AppleScript Export Script
  7. Fix 4: A Dedicated Exporter (Apple Notes Exporter Pro)
  8. All Four Options Compared
  9. Which One Should You Actually Use?
  10. Sources
  11. FAQ

What Apple Actually Documents

Apple's own support guide for importing, exporting, and printing notes is specific about this, once you read the import and export sections side by side. For import, Apple tells you to select a folder and “click Preserve folder structure on import to keep the imported notes organized the way they were in the folder.” That is an explicit, named checkbox for a specific behavior.

What's missing from the export instructions
For exporting, Apple's guide says only to select the notes you want and choose File > Export as > Markdown. There is no mention of folder structure at all, and no equivalent checkbox. The feature exists in one direction and not the other.

That asymmetry is confirmed directly from Apple's documentation, not a third-party guess. It also lines up with what people actually experience: multi-select a batch of notes from different folders, export them, and the result is every file sitting together in whichever destination folder you picked on your Mac, with nothing to indicate which Notes folder each one used to live in.

What a Flattened Export Actually Looks Like

Say your Notes app has three folders: Work, Recipes, and Personal, with a combined 40 notes across them. Select all 40 and export to Markdown, and you get one folder on your Mac containing 40 individual .md files (plus an Attachments subfolder per note that has images). Nothing in that output tells you which three came from Recipes and which nine came from Work, beyond whatever each note's own title happens to say. If two notes in different folders happen to share a title, one will also silently overwrite the other in that shared destination, a separate but related risk worth knowing about before a large export.

Why Import Gets This Feature and Export Doesn't

Apple has not explained this design choice anywhere we could find, so take this as reasoning rather than a confirmed answer. Import already has a natural destination: your existing Notes folders. Telling the app to match incoming files to folders that already exist is a well-defined problem. Export starts with no destination until you pick one on the spot, so recreating a matching folder tree there is a meaningfully bigger feature to build, and a plain flat dump of files at least gets your content out of Notes, which was likely the actual point of shipping the feature in the first place.

Fix 1: Export One Folder at a Time (Free, Manual)

The simplest fix costs nothing and needs no extra software: stop exporting your whole library in one action, and export one Notes folder at a time instead.

  1. Open a single folder in the Notes sidebar, not a merged view like All iCloud.
  2. Select every note inside it (Cmd-A, or Cmd-click each one).
  3. Choose File > Export as > Markdown (or PDF), and save that batch into a new folder on your Mac named after the original, for example Recipes.
  4. Repeat for every folder in your library.
Where this falls short
It fully preserves your top-level organization, but it does not automatically recreate nested sub-folders if you use them inside Notes, you would need to repeat the process one level deeper for those too. It also does not scale well much past a handful of folders; ten folders means ten separate export actions instead of one.

Fix 2: A Free Open-Source Tool That Automates It

If manual, folder-by-folder exporting is too much repetition, kzaremski/apple-notes-exporter is a free, open-source Mac app (GPLv3 license, roughly 680 GitHub stars as of this writing) built specifically to bulk-export Apple Notes, including iCloud notes, while recreating your original folder structure automatically. It supports 18 output formats, well beyond Apple's own Markdown and PDF, and ships as a notarized, ready-to-run .app download rather than something you have to compile yourself in Xcode.

It is a genuinely solid option if you are comfortable installing an app from a GitHub releases page rather than the Mac App Store, and you only need to export once or occasionally rather than run scheduled, repeatable backups.

Fix 3: DIY with an AppleScript Export Script

If you are comfortable with scripts and the Terminal, a handful of community AppleScript-based exporters, such as notes2md and similar small projects on GitHub, read notes directly out of the Notes app's own AppleScript dictionary and write them out with a folder for each Notes folder. This route gives you the most control, since you can usually adjust the script yourself, but it comes with the most setup: cloning a repository, installing a runtime like Python or Ruby if the script needs one, and troubleshooting anything that breaks on your own without vendor support if Apple changes something in a future release.

Fix 4: A Dedicated Exporter (Apple Notes Exporter Pro)

Apple Notes Exporter Pro takes the same idea as the free options, reading notes directly rather than going through Apple's own export dialog, and packages it as a paid, one-time $14.99 app: select your whole library or specific folders, choose from ten output formats (PDF, Word, Markdown, HTML, Plain Text, RTF, EPUB, LaTeX, JSON, JSONL), and your original folder hierarchy is recreated in the output automatically. It also adds scheduled backups (daily, weekly, or monthly) that neither the manual method nor the free tools offer out of the box, which matters if you want this handled once and then forgotten rather than repeated by hand every time.

All Four Options Compared

OptionKeeps foldersCostEffort
Native export, all notes at onceNo, everything flatFreeLowest, one export
Native export, one folder at a timeYes, top-level onlyFreeMedium, one export per folder
kzaremski/apple-notes-exporter (OSS)Yes, automaticFreeLow, one-time install from GitHub
Apple Notes Exporter ProYes, automatic$14.99 one-timeLowest, one export

Which One Should You Actually Use?

If you only have two or three folders and export rarely, the manual folder-by-folder method costs you nothing but a few extra minutes and is genuinely the right call, there is no reason to install anything for that. If you have a deep or wide folder tree, want more export formats than Markdown and PDF, and are comfortable installing an app from GitHub, kzaremski/apple-notes-exporter is a strong free choice and, for a lot of people, the best option on this list. Apple Notes Exporter Pro earns its price specifically when you want this to be a no-setup, one-click action, need formats like Word or EPUB alongside Markdown, or want it to happen again automatically on a schedule without you remembering to run it.

Sources

Apple's own documentation: Apple Support, importing, exporting, and printing notes, which describes the “Preserve folder structure on import” option with no matching export equivalent.

Feature background: MacRumors, importing and exporting Markdown files in Apple Notes.

Free open-source alternative: kzaremski/apple-notes-exporter on GitHub.

Our own coverage of the feature itself: Apple Notes’ native Markdown export vs Exporter Pro, and the separate bulk-export data corruption bug worth checking before a large export.

Frequently Asked Questions

Does Apple Notes preserve folder structure when exporting to Markdown?
No, not on a bulk export. Select several notes from different folders, choose File > Export as > Markdown, and every file lands together in the one destination folder you pick. There is no option in the export dialog to recreate your Notes folders on the way out, and Apple's own support documentation only describes a "Preserve folder structure on import" option, with no equivalent for export.
Why does Apple only offer folder preservation for import, not export?
Apple has not explained the decision publicly, so this is informed reasoning rather than a confirmed reason. Import already has a natural destination, your existing Notes folders, so recreating structure there is a matter of matching files to folders that already exist. Export has no such destination until you pick one, and building a full folder-recreation feature for a one-off export action was apparently deprioritized against a plain flat-file dump that at least gets the content out.
Are my exported notes actually lost or mixed up together?
No, nothing is lost. Every note exports as its own separate file, and multi-select export even groups them into one destination folder rather than scattering them randomly. What is missing is only the higher-level organization, which folder each note came from. A hundred notes from five different folders become a hundred files sitting side by side with no indication of their original grouping beyond whatever is in each note's own title or content.
Can I export one Apple Notes folder at a time instead?
Yes, and this is the free, no-extra-software fix. Open one folder in Notes, select all the notes inside it, export that batch to its own destination folder named after the original, then repeat for every folder in your library. It fully preserves your top-level organization at the cost of doing the export step once per folder instead of once total, and it does not carry over sub-folder nesting if you use nested folders in Notes.
Is there a free tool that preserves Apple Notes folder structure automatically?
Yes. kzaremski/apple-notes-exporter is a free, open-source (GPLv3) Mac app that bulk-exports Apple Notes, including iCloud notes, to 18 formats while recreating the original folder structure automatically. It has a notarized, downloadable build rather than requiring you to compile it yourself, and roughly 680 GitHub stars as of this writing. It is a legitimate option if you are comfortable installing an app from GitHub rather than the Mac App Store and do not need scheduled, repeatable backups.
What is the fastest way to export Apple Notes and keep folders intact?
A dedicated export tool built to preserve structure automatically, so you do not do it by hand or maintain a script. Apple Notes Exporter Pro reads your notes directly, recreates your folder hierarchy in the export, and supports ten output formats plus scheduled backups, for a one-time $14.99. The manual folder-by-folder method and the free kzaremski/apple-notes-exporter tool both get the same result at no cost, in exchange for more manual steps or more setup.

The Bottom Line

Apple Notes' native export gets your content out, but it does not carry your organization with it: a flat file dump is what it produces, confirmed by Apple's own documentation offering folder preservation only on the way in. Exporting one folder at a time costs nothing and works fine for a small library. For anything bigger, a free open-source tool or a dedicated exporter that recreates the structure automatically will save you far more time than the few dollars or minutes either one asks for.

Keep reading: see what else the native Markdown export gets right and wrong beyond folders, check the separate data corruption bug on large bulk exports before you run one, see why a checklist can break on re-import, walk through our batch export workflow for Apple Notes folders, or browse every Apple Notes export and backup guide.

Want Your Folders to Survive the Export?

Apple Notes Exporter Pro reads your notes directly and recreates your original folder structure automatically, with ten export formats and scheduled backups included.

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