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Encrypting 🔐 a Home 🏡 in Raspberry Pi
May 24, 2021
4 minutes read

;tldr Use fscrypt to encrypt your home partition, with a few simple steps.

Why encryption?

I prefer to encrypt all my (and my family’s) storage at rest. Encryption is useful in scenarios where someone gains physical access to your device. This may save you from any losses other than the material cost of the device. Specially with a Raspberry Pi, it is more of a worry as how tiny the device is (the SD card is even smaller). It is much less likely that you lose your desktop tower. Its worrying how many people carry around their portable computing devices (phones/laptops/tables) around without encryption at rest.

This allowed me to safely RMA a failed SD card. If I hadn’t encrypted the data, I would have had to destroy an expensive SD card. Could as easily happen with any other portable device.

Encrypting the Pi

Both Manjaro or Raspbian do not encrypt by default. To get around that, I have been relying on ecryptfs to encrypt my sensitive directories. Recently though, I switched to using fscrypt, which ext4 and f2fs support natively in most recent kernels. The goal of this post is to outline the key steps to get usable encryption working with the Pi.

Enable encrypt feature flag

If you are already on ext4 / f2fs, you can simply enable the encrypt feature flag:

tune2fs -O encrypt /dev/mmcblk0p2

/dev/mmcblk0p2 here is the mount point for my root file system.

Install fscrypt

To be able to use fscrypt, you’ll need to install the userspace tools. On Arch/Manjaro:

$ pacman -S fscrypt

On Debian/Raspbian:

$ apt install fscrypt libpam-fscrypt

Setup fscrypt

To setup fscrypt, I’d recommend you to login as root, without any session running as your target user (say penguin).

[email protected]:/home# fscrypt setup
Defaulting to policy_version 2 because kernel supports it.
Customizing passphrase hashing difficulty for this system...
Created global config file at "/etc/fscrypt.conf".
Metadata directories created at "/.fscrypt".

Configure the new home directory

[email protected]:/home# mkdir /home/penguin-new-home
[email protected]:/home# fscrypt encrypt penguin-new-home --user=penguin

When prompted, choose 1 (pam_passphrase) to decrypt using the login password:

The following protector sources are available:
1 - Your login passphrase (pam_passphrase)
2 - A custom passphrase (custom_passphrase)
3 - A raw 256-bit key (raw_key)
Enter the source number for the new protector [2 - custom_passphrase]: 1

IMPORTANT: Before continuing, ensure you have properly set up your system for
           login protectors.  See

Enter login passphrase for penguin:
"penguin-new-home" is now encrypted, unlocked, and ready for use.

Copy over the contents to the new encrypted directory:

[email protected]:/home# cp -a -T /home/penguin /home/penguin-new-home

Test the encryption 🤞:

[email protected]:/home# echo foo > penguine-new-home/bar
[email protected]:/home# fscrypt lock penguin-new-home --user=penguin
"penguin-new-home" is now locked.
[email protected]:/home# ls penguin-new-home/bar
ls: cannot access 'penguin-new-home/bar': No such file or directory
[email protected]:/home# fscrypt unlock penguin-new-home
Enter login passphrase for penguin:
"penguin-new-home" is now unlocked and ready for use.
[email protected]:/home# cat penguin-new-home/bar

Great, encryption works!

If you also plan to login directly to your Pi (without SSH), would recommend using the PAM Module on Manjaro/Arch to automatically unlock the directory. It also will allow you to keep your home directory’s passphrase in sync with changes to the login passphrase. On Debian, libpam-fscrypt should have already configured PAM.

You can test this by logging in as penguin on a reboot. Observe that the home directory should be decrypted.

Now you may move the encrypted directory as the home.

[email protected]:/home# mv penguin penguin.bk
[email protected]:/home# mv penguin-new-home penguin

Test if everything in the system works as per your liking and then remove /home/penguin.bk.

Although, if the existing home had data, the content may still be recoverable. Would recommend wiping the free space.

Remote Access

Because the ssh daemon needs access to /home/penguin/.ssh/authorized_keys, you will not be able to login remotely. To get around this, we have to move our authorized_keys file on the unencrypted space. Create a file /etc/ssh/sshd_config.d/overrides.conf with the following content:

AuthorizedKeysFile      .ssh/authorized_keys  /etc/ssh/authorized_keys/%u
PasswordAuthentication  no

This adds /etc/ssh/authorized_keys/<user> as a file to look for a user’s authorized keys. You can maintain the authorized keys in /etc/ssh/authorized_keys/penguin:

[email protected]:/# mkdir /etc/ssh/authorized_keys
[email protected]:/# cp /home/penguin/.ssh/authorized_keys /etc/ssh/authorized_keys/penguin
[email protected]:/# chown penguin /etc/ssh/authorized_keys/penguin
[email protected]:/# chmod 600 /etc/ssh/authorized_keys/penguin
[email protected]:/# ln -sf /etc/ssh/authorized_keys/penguin /home/penguin/.ssh/authorized_keys
[email protected]:/# systemctl restart sshd

SSH should now work again! If you work with tmux, you can automatically decrypt before logging in:

ssh [email protected] -t -- 'fscrypt unlock /home/penguin; tmux -u new -As pi'


  1. Encrypting of files on a Pi can impact the system performance, as encryption/decryption needs the CPU. If you need to do a lot of disk IO (eg: build files), I’d recommend moving those operations to an unencrypted directory or the memory.
  2. Only the home directory is encrypted, so rest is still vulnerable. Someone could get an hold of your SSL certificates, ZeroTier token, WireGuard token. Ensure these are on an encrypted directory as much as possible. In case of a disk loss, review your backups to rotate all the keys.
  3. This doesn’t protect you from an attack in a running machine, so use a firewall. I’d recommend ufw.


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