A technique to manage software licensing in an environment that provides virtual desktop infrastructure (VDI). A license manager is configured to receive first information identifying software applications associated with a virtual machine template used in the infrastructure, as well as second information that a user has logged into the VDI from a client device, thereby creating a VDI session. For a particular time period of interest, the license manager calculates software application usage information from the first and second information. Preferably, the software application usage information represents an application count that is based on the user and the client device “pair” when the user has the VDI session during at least some portion of the time period. The software application usage information is provided to one or more other computing systems to take a given action, such as tracking, managing, auditing, enforcing and accounting for software usage in the VDI environment.