This paper brings forth the experiences and lessons of implementing a participatory modelling process, the Companion Modelling (ComMod) approach, to a natural resource management system in the province of Palawan, Philippines. In this study, we explore the added value of using ComMod in a research and development project, and then we describe the actual modelling process, which includes the use of multiple methods for its evaluation, namely, workshop evaluation exercises, criteria & indicators for the project and the ComMod evaluation protocol. We use the lessons of this evaluation to assess the organisational learning and discuss the role of the modelling process within the development project.