Hi,
Here is the procedure specifically for Joplin Desktop running on Linux, migrating from Dropbox to a self-hosted Joplin Server while preserving end-to-end encryption.
Migrating Joplin from Dropbox to Joplin Server on Linux
Step-by-step instructions with end-to-end encryption enabled
These instructions explain how to move an existing Joplin installation on Linux from Dropbox synchronization to Joplin Server while preserving notes, notebooks, attachments, and end-to-end encryption (E2EE).
Important: Do not delete the Dropbox data, disable encryption, or remove the existing Joplin profile until the migration is complete and verified.
Step 1 — Synchronize Joplin with Dropbox
On the Linux computer currently running Joplin:
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Open Joplin Desktop.
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Click Synchronize to synchronize with Dropbox.
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Wait until synchronization finishes.
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Verify that all notebooks, notes, and attachments are present.
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Check for synchronization errors and resolve any before proceeding.
If Joplin is also installed on other computers or mobile devices, synchronize those devices with Dropbox first. Then synchronize the Linux computer again to obtain their latest changes.
The Linux computer should have a complete, up-to-date copy of the notes before changing synchronization providers.
Step 2 — Back up the Joplin data
Create two backups before making any changes.
A. Export all notes to JEX
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Open Joplin Desktop.
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Select File → Export All → JEX (Joplin Export File).
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Save the JEX file somewhere safe, preferably on another drive.
A JEX export preserves notebooks, notes, and attachments, but it is not a complete backup of Joplin's configuration and encryption settings.
B. Back up the entire Joplin profile
On Linux, the default Joplin Desktop profile is located at:
~/.config/joplin-desktop
Close Joplin completely before copying the profile.
Open a terminal and run:
mkdir -p ~/Joplin-Backup
cp -a ~/.config/joplin-desktop \
~/Joplin-Backup/
This copies the entire Joplin profile, including its database, settings, and encryption-related information.
Note: If Joplin was installed using Flatpak or a custom profile directory, its profile may be stored elsewhere. Confirm the actual profile location before running the backup command.
Do not import the JEX backup into the existing profile during migration, as doing so can create duplicate notes.
Step 3 — Prepare Joplin Server
The new Joplin Server must already be installed, configured, and accessible from the Linux computer.
Obtain the following information:
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Server URL: For example, https://joplin.example.com
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Username or email: The Joplin Server account
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Password: The Joplin Server account password
The Joplin Server account password is separate from the Joplin end-to-end encryption password.
Make sure the server account has sufficient storage capacity for all notes and attachments.
Step 4 — Change the synchronization target
On the Linux computer:
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Open Joplin Desktop.
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Select Tools → Options.
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Select Synchronization.
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Change the synchronization target from Dropbox to Joplin Server.
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Enter the Joplin Server URL.
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Enter the account username/email and password.
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Click Check synchronization configuration, if available.
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Save or apply the settings.
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Return to the main Joplin window.
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Click Synchronize.
Joplin should begin uploading the existing notes, notebooks, and attachments to the new server.
Important: Changing the synchronization target is not the same as deleting or recreating the notes. The existing local Joplin database remains in place.
The initial synchronization can take considerable time, especially if there are many attachments.
Allow it to finish without interrupting Joplin.
Step 5 — Verify end-to-end encryption
This step is particularly important because the existing Dropbox synchronization uses E2EE.
After changing synchronization targets:
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Open Tools → Options → Encryption.
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Verify that end-to-end encryption is enabled.
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Confirm that the existing encryption master key is still present.
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Confirm that the master key has a valid password.
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If E2EE has become disabled, re-enable it using the existing encryption configuration where possible.
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Synchronize again and allow the process to finish.
Do not deliberately delete the existing encryption keys or create new ones during this migration.
The person should retain the existing E2EE password. They may need it when connecting other devices.
If encryption must be re-enabled, Joplin may need to upload encrypted versions of existing data again.
Do not proceed until the encryption configuration is correct and synchronization completes successfully.
Step 6 — Connect additional devices
After the Linux computer has synchronized successfully with Joplin Server, configure the other devices.
For each additional computer, Android phone, iPhone, or tablet:
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Open Joplin.
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Confirm that any pending changes were previously synchronized to Dropbox.
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Open the synchronization settings.
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Change the synchronization target from Dropbox to Joplin Server.
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Enter the Joplin Server URL and account credentials.
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Start synchronization.
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If prompted, enter the existing end-to-end encryption password.
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Allow synchronization and decryption to finish.
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Verify that notebooks, notes, and attachments are accessible.
Connect one device at a time, allowing synchronization to finish before proceeding to the next.
If Joplin displays a warning about deleting local notes or an unexpected large number of deletions, stop and investigate rather than accepting the changes.
Step 7 — Verify the migration
Before discontinuing Dropbox synchronization, verify the following:
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All notebooks are present on the Linux computer.
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Notes contain the expected text and images.
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PDFs and other attachments open correctly.
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End-to-end encryption remains enabled.
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No encryption keys are missing.
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Synchronization finishes without errors.
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All additional devices can synchronize with Joplin Server.
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A new test note created on one device appears on another device.
A successful initial upload alone does not guarantee that the migration is complete. Verify that changes synchronize correctly between devices.
Step 8 — Retire Dropbox synchronization
Once the migration is complete and verified, Dropbox is no longer needed as Joplin's synchronization provider.
The old synchronization data is generally stored in:
Dropbox/Apps/Joplin
This is the Dropbox cloud folder, not necessarily a folder in the Linux home directory.
Leave the Dropbox data intact for a while as an additional precaution.
After confirming that all devices are using Joplin Server and that the migration was successful, the old Dropbox synchronization folder can be deleted if it is no longer needed.
Important recommendations
Keep end-to-end encryption enabled. There is normally no reason to disable encryption merely to change synchronization providers.
Keep both backups. The JEX export provides a convenient notes backup, while the full Linux profile backup preserves configuration and encryption-related information.
Do not import the JEX backup during a normal migration. The existing Joplin profile already contains the notes that need to be uploaded.
Do not configure multiple devices simultaneously. Complete the initial synchronization on Linux before connecting other devices.
Do not delete Dropbox data prematurely. Retain it until the new server has been tested thoroughly.
Official Joplin documentation
Final recommendation: Use the existing Linux Joplin Desktop profile to perform the migration. Back it up, change the synchronization target to Joplin Server, verify encryption, and then migrate the remaining devices individually. This avoids unnecessary exporting, importing, and rebuilding of the note collection.