Software is managed in a virtual desktop environment by discovering virtual appliances contained in the virtual desktop environment, and for each virtual appliance discovering the virtual machines belonging to the virtual appliance. Software is further managed by discovering the standalone virtual machines comprised in the virtual desktop environment, and for each discovered virtual machine, introspecting each virtual machine to detect non-virtual applications and virtualized applications running in the virtual machine. For each detected application, identification is made of the operating system on which the application is running.