Compacting a VirtualBox VDI image

Firstly, you’ll need to install zerofree on your Linux image, then mount the root partition as a read only volume. This can be done via:

sudo apt-get install zerofree
sudo apt-get clean
sudo reboot
# interrupt grub boot and boot into recovery mode
mount -n -o remount,ro -t ext4 /dev/sda1 /
zerofree /dev/sda1
shutdown -h now

And now on the Windows Host:

"C:\Program Files\Oracle\VirtualBox\VBoxManage.exe" modifyvdi "VirtualBox VMs\server\server.vdi" compact

This should make the VirtualBox image more in line with the calculated size it should be.