This paper introduces a system identification approach to overcome the problem of insufficient data when developing and parameterising an agroforestry system model. Typically, for these complex systems the number of available data points from actual systems is less than the number of parameters in a (process-based) model. In this paper, we follow a constrained parameter optimization approach, in which the constraints are found from literature or are given by experts. Given the limited a priori systems knowledge and very limited data sets, after decomposition of the parameter estimation problem and after model adaptation, we were able to produce an acceptable correspondence with validation data from a real-world agroforestry experiment.