The mechanisms shaping biodiversity in agroecosystems and particularly in agroforestry are difficult to understand and predict. The relation between planned biodiversity, the species chosen by the farmer, and associated biodiversity, the species that are able to adapt and thrive in agroforestry systems, is determined by diverse biological, environmental and management variables. Most studies in this area rely on case studies within specific biogeographical zones, species combinations and management options, which hampers drawing general conclusions. This chapter describes a modelling approach to compare associated biodiversity in different agroecosystems. Results show the relevance of alley cropping and intercropping to increase associated biodiversity in agricultural landscapes. The chapter also highlights the importance of further research to guide environmental managers and practitioners in applying the best policies for biodiversity conservation in agricultural landscapes.