Research and Technology Organizations (RTOs) are knowledge-intensive firms. They tend to rely mainly on their employees and their individual competencies (codified or non-codified), the networks and communities they are involved in as well as the structural resources of the organization itself. These resources, mainly of intangible nature, are expected to play an important role on the innovation capabilities of RTOs, but tend to be neglected in the traditional performance reporting and management systems. The main motivation for this research is to foster the introduction of an intangible measurement system in the RTO under investigation. This paper illustrates the application of an innovative approach, for the design of a performance measurement system in a RTO. The process of collection and reporting of intangible indicators is defined and validated by relying on an in-house approach and related tool, called EFFICENT.