This is remarkably simple! First, BACK UP YOUR DB.
Backed up? Good. You dont need to back your web files up if they are being mounted from a shared folder.
Open your puPHPet config.yml, scroll down to the php section, and change version from ’55’ to ’56’, and save it.
Next, type vagrant destroy, to remove the old stuff, and then vagrant up, which will re-initialise the server with your shiny new PHP version!