How to encrypt Kali Linux after install?

As Kali Linux is based upon Debian, instructions for encrypting an existing Debian install should be valid. These instructions are from the Setting up encryption after debian wheezy install question. I did some basic testing, and it seems to be a working solution (last tested on Kali 2016.2).

First install ecryptfs-utils (it may already be installed)

sudo apt-get install ecryptfs-utils

then boot to recovery mode and as root run

ecryptfs-migrate-home -u your_user_to_migrate

After the script runs, log out and log in as your user

exit

You might also with to run

ecryptfs-unwrap-passphrase

enter your use password when prompted and save the information in a safe place in the event you need to perform data recovery.

Last you can delete the temp files / directories created by the migration script and reboot (technically you do not need to reboot).

Another tool - kali.org/tools/ccrypt/