At NIAB, a UK based company that provides research, services and information to the agricultural and food sector, a system has been designed that helps to assess and manage the growing research programme of the company. Since the company was ‘privatised’ four years ago, research activities have increased and moved away from solely applied research to a mix of applied and more fundamental research. Being a key element of the new developed company strategy, research now plays an increasing important role in broadening the scope of the company and keeping current services competitive by driving innovation. All research at NIAB is externally funded. In this paper we report on the process to design NIAB’s performance measurement system, for which the Performance measurement system Systematic Design Approach was used. The design process was started with an elaborate structured problem analysis of the research process and its inter and extra–organisational context. Based upon this analysis, firstly a conceptual and secondly a detail design of a performance measurement system was made. To maximise the leverage from research, the system has been designed to optimise the value delivered to the funder as well as the value delivered to internal customers in the form of knowledge that drives innovation.