Which Note-Taking Apps Keep Your Notes as Plain Markdown Files

With Obsidian and Notable, your notes are saved as plain Markdown files; you can access them at any time and from anywhere without needing to use either app. A program that allows you to export your Markdown notes has different benefits than using the actual app that you create your notes in: when that program exports your notes, it is exporting a converted version of the original file on your computer. When making the choice between an app to use for editing your notes and a program that will export your notes, it is essential to understand the implications of this when changing editors.

Although plain files don’t guarantee a perfect transition between apps (i.e., you will not have all of the images, attachments, and hyperlinks), knowing how to access the Markdown notes you edit from each app on your tablet or iPhone is the first step to making your transition successful. When deciding which Markdown note-taking app you want to use on your iPad, Mac, or Samsung Galaxy S phone, check to see how the app allows you to export or access your files. If the only way to export your notes is from the computer, it could be a significant issue if you only use a tablet or phone to take notes. Once you know how to separate the notes you create from the files you export, you are on your way to a smooth transition!

Does Your Notes App Store Plain Markdown Files, or Just Export Them?

Notes stored locally, or “offline,” can either be stored as a standalone database (in which case you’d have a local SQLite database on your device with all your notes in one place in the app), or they can be stored in separate files (in this case you would have many different markdown files that can be written on and still be part of a single working document). Joplin is an example of a note-taking app that does both; its mobile and desktop apps use a local SQLite database where all your notes are kept together and not stored as individual markdown files. Bear’s note-taking app is similar – it also uses SQLite to store all your notes locally in iOS and macOS. Joplin’s storage architecture describes exactly that. Bear’s storage documentation likewise describes SQLite on iOS and macOS.

A couple of other good examples are Notion and Obsidian; both applications are used to create a working note and have an option to export the content as a markdown file like Notion creates Markdown through export. However, if you were to edit the exported copy of Notion, it would not edit the original Notion page.

When deciding which note-taking software is best for you, consider what features you want in your note-taking software. Do you want a note-taking app that allows you to collaborate with other users on the same working document? Or do you just need a useful copy of your working document so that you can work on it from another location?

Where the Files Actually Live, and What Else Is in That Folder

The collection of your working notes with file-based notes is a folder rather than an exported destination. In Obsidian, that folder is called a vault and is used as a storage item. The folder where you keep your notes has an .obsidian file hidden within it, which is used to store configurations, themes, and plugins that are specific to the vault you created. In addition, there are global configurations for the application that are stored in a separate System Folder. Obsidian advises you not to create a vault in the system folder because it could lead to corruption of your data or loss of data. The storage documentation separates the notes from the hidden .obsidian folder.

Those distinctions matter when you copy a collection:

• The .md files carry the written notes.
• Image, PDF and other attachment files carry content that isn’t inside the note’s text.
• The .obsidian folder carries the Obsidian setup, not an extra copy of your writing.

The metadata cache serves as the “general index” for functionality like Obsidian’s graph and outline and Obsidian documents how to build that index back up from the underlying files. Do not confuse rebuilding the index with valuing your actual notes.

Notable makes it particularly clear how the two differ. Their published Desktop tutorial separates Markdown files into a ‘notes’ subfolder, and attachment files into an ‘attachments’ subfolder. The front matter is written at the top of the Markdown file as text fields; while another editor may read these text fields, it is possible that the editor may handle these fields differently. So if you were to copy a subfolder of notes, the attachment files will remain at their original file location.

Can your phone reach the same files?

A familiar editor does not violate the operating systems folder restrictions. For an Obsidian vault stored on iCloud using an iPhone or iPad, iCloud’s instructions indicate that the vault will be located in the iCloud Drive Obsidian folder. To find your vault from within the Files application, select Browse → iCloud Drive → Obsidian; any other folders that have similar names will not have the same documented contents as the folder you will find.

When evaluating note taking apps for the iPad, verify if a second editor (someone using the iPad as well) can access the actual file inside of the app. While a shortcut for a heading or a visually appealing preview of what is being edited illustrates how an app makes changes to the text inside of it, they do not indicate where the final product will be saved.

The Exact Export Path for Each App — and What Doesn’t Come Out With It

Copy originals and send any exports to the new folder. The matrix is based on vendor documentation and published Joplin source code, not based on a hands-on test with seven applications. Tools for each of the devices will differ depending on whether you are exporting from file-based applications, so for file-based apps, you’ll want to copy the current collection and not convert it again.

Apple’s guides that are currently linked are for macOS 27, iOS 27 and iPadOS 27; if you have an older Apple operating system, you will need to select the type of operating system you are using via the version selector. When you are using either an iPhone or an iPad, you may be able to access the Markdown option in the View More button if it is available. Joplin’s mobile bulk-export button produces JEX, not the desktop Markdown folder shown above.

Check the whole-collection route separately

The path to bulk exporting your entire Notion workspace is as follows: On the desktop app or through the web interface, click the Settings option, followed by the Workspace option, then General, and then Export All Workspace Content. All pages that you do not have access to will be excluded from this export, and any restrictions imposed on the workspace or teamspace may limit your ability to export content from it. In order for guests to be able to export any content, they must have Full Access to that particular page or database; just because a guest has a visible page to export does not mean that they have access to all of the pages in your workspace.

The steps to perform a bulk export of Bear varies between their different platforms. On Mac:

1. Select Notes in the sidebar.
2. Press Command-A to select all notes in the list.
3. Choose File → Export notes… and select the export format.

On iPhone or iPad:

1. Select Notes in the sidebar.
2. Tap the Notes title with its arrow at the top.
3. Tap Export… and select the export format.

Read the output, not just the success message

Podfeet produced an iPadOS 26 export of Apple Notes in October 2025 as part of their walkthrough for the program. In that export, there was text and a separate folder for attachments. The image shown in both 1Writer and MWeb displayed appropriately. In contrast, the underline feature in 1Writer generated double-plus markup, which 1Writer incorrectly reported as literal. Additionally, the same numbered list rendered differently in each of the two applications. The previous examples demonstrate the variation between external runs, not simply the results of every Apple Notes export created to date; they also illustrate why a saved export versus faithful rendering of content should be verified independently.

A backup isn’t necessarily your portable copy

According to Joplin’s documentation, JEX backups are designed to back up notes and metadata (to facilitate re-importing into Joplin) when the JEX option is used, while Markdown is to be selected when the notes will be used outside of Joplin.

Bear warns you not to restore a backup just to look at it. The Backup Instructions say that restoring a backup will delete ALL your current notes (including your trash) and replace all those with whatever is included in the backup. Instead:

1. Make a copy of the .bear2bk backup and leave the original untouched.
2. Change the copy’s extension to .zip, then uncompress it in Finder or Files.
3. Inspect the resulting .textbundle packages, one per note. A TextBundle package keeps its text file and any assets together; preserve that structure.

Encrypted notes in a Bear backup still require their password. Extraction isn’t a way around that requirement.

When a Markdown App Stops Using Markdown Files

A storage recommendation can go stale even when an app keeps its name and familiar editor. Logseq’s April 2026 product-split announcement separates two choices:

• Logseq OG keeps file-based Markdown graphs. The team says it will receive maintenance updates, but not new features.
• The main Logseq app uses database graphs and receives the new feature development. Existing users aren’t required to migrate.

Logseq’s published mirror design states that it has a feature for writing derived markdown files under the graph’s “mirror/markdown” folder on the desktop. However, the database is still used as a “working store,” and specifically states that those generated markdown files are not allowed to be read back into the graph. It also specifies that the browser/builds and mobile builds cannot access this filesystem feature.

With respect to this design, although other tools receive markdown files that are readable by them, this does not represent the same arrangement as editing an Obsidian Note. If you were to change a generated mirror, you could not expect that your edits would return to the app. The current roadmap outlines the development of a two-way sync between markdown and the database and indicates that the product is currently in beta-testing status, but a roadmap entry does not guarantee that your installed build of Logseq will support this feature.

You should keep the original collection when changing graph types and only use disposable materials to test new models. The question is not if Logseq can generate markdown files, but rather whether your specific graph uses markdown files as working notes, produces them as output, or facilitates documentation bridging the two.

What You Give Up Either Way, and How to Check It Yourself

If it works for you to have an app-managed library, that library should allow you to edit and organize your notes the way you want to, and when you export your notes from that library, those exports should contain everything you need. You have to pay to maintain your library by keeping its exports current and ensuring those exports remain accessible whenever your notes become more complicated. Being able to work with Markdown files means you can bypass the need to convert Markdown files for use as future copies of your notes; however, you are still responsible for managing attachments, ensuring your links are compatible, configuring your library’s settings, and managing the sync method that will make your notes accessible on your various devices.

You will still need to back up your notes regardless of what library solution you choose, and as explained in Obsidian’s backup guidance, the ability to sync up between devices to carry changes is separate from making a separate backup copy of the notes. A folder that appears on your laptop as well as a folder on your phone does not mean you have backed up your notes; it only indicates that you has a synced version of the folder with the same changes.

Try this with disposable notes

1. Create a test note containing a heading, bulleted list, small table, image and tag. Make a second note and link to it if the app supports note-to-note links. Add a drawing or multipage scan if those are part of your normal notes.
2. Use the applicable path in the table to export the test notes, or copy their working files and attachments into a new folder. Unpack ZIP downloads there. Keep the originals unchanged; don’t rename or reorganize the output yet.
3. If the output is Markdown, open it in a plain-text editor outside the source app. Check the words, formatting marks and expected tags or metadata. If you only have ENEX, HTML or JEX, stop here: you still need a Markdown conversion route.
4. Open the exported image or scan separately. Then open the collection in your intended replacement app and follow the link to the second note. A filename appearing in the text isn’t proof that its attachment or destination is present.
5. If direct outside editing matters and the app documents working-file access, create one more disposable note. Change one word in its working file with another editor, then reopen it in the source app. Don’t edit databases, internal sync files or generated output.
6. Repeat the access and opening checks on the phone, tablet or browser you actually rely on. If the export requires a computer, establish that you have access to one before depending on that route.

Selecting the best note-taking app for Android requires more than merely viewing a desktop export list. In addition, a successful export is not sufficient to demonstrate that you have a complete set of notes in your collection; therefore, before deleting the original documents of exported notes and attachments, it is critical to compare the two. Finally, choose a storage option that reflects the amount of work you are prepared to continue to do, rather than simply the storage option that appears to have been designed to support plain-text files only.

Where the file lives decides what you can do next

A Working markdown file and you can also change your editor(s) without needing to create a new copy from the original application that created it. Exports provide an alternative means of escaping to an easier format but your destination, available device and what files were archived will determine if they are useful in your particular situation. Retain the original collection until you have: Opened the text. Checked attachments. Followed links to outside sources, if any.

FAQ

What if Windows won’t open my Notion export?

Notion’s ZIP troubleshooting has indicated long, deeply nested file paths may be a possible cause of a problem, so export again with the ‘Create folders for subpages’ option unchecked, or try using an application like 7-Zip to extract the ZIP files instead of using Windows Explorer or similar applications.