In this paper we focus on the governance, in particular evaluation and monitoring, of the growing number of transdisciplinary collaborations (TDC’s). Researchers and a variety of stakeholders collaborate in such TDC’s, the purpose of which is to address societal challenges, like renewable energy, healthy aging or better language teaching in schools. Commonly used practices for evaluation of scientific research (accountability, rankings and benchmarking, dedicated to scientific excellence) do not fit the goals of TDC’s. A bottom up or stakeholder oriented approach is better suited; one that stimulates mutual learning as well as the development of socially robust knowledge. We introduce the participatory impact pathways analysis (PIPA), as a method that suits the requirements. It has been developed in the context of development research. Two crucial features are the involvement of stakeholders from the start, and the joint development of a theory of change. This narrates what one wants to achieve and how that will be achieved. From this, stakeholders construct a logical frame that serves as a source for indicators. These indicators enable monitoring ex durante, during the TDC. We present evidence of the use of PIPA for a TDC. From this empirical evidence a number of issues with regard to evaluation, monitoring and indicators can be identified that require attention. Most prominent is the change of function of indicators. Instead of looking back and a focus on past performance, indicators look forward, in the short, intermediate and more distant future.