Embodiments of the invention relate to post-install configuration of virtual appliances in a virtual machine. A packaging and distribution format is provided with two tools to support the configuration of the virtual machine. The first tool is employed to support configuration of the virtual machine, and employs an activation script during a boot operation. The second tool is employed by a call from the first tool. The second tool configures a virtual application in communication with the virtual machine with use of a configuration script. The configuration script is separate from the activation script and disassociated from an image binary of the virtual machine. The disassociation of the configuration script from the activation script supports changes to the configuration script without affecting the image binary.