Agricultural management is a major factor driving the change of faunal richness in anthropogenic landscapes. Thus, there is an urgent need to develop tools that allow decision-makers to understand better intended and unintended effects of agricultural policy measures on biodiversity. Here we demonstrate the potential of such a tool by combining a socio-economic model with the biodiversity model GEPARD to forecast the response of bird and carabid species richness to two scenarios of agricultural subsidies: (1) subsidies based on production levels and prices and (2) direct income support that is independent of production levels. We focussed on farmland of the Lahn-Dill area, Germany, as an example of European regions with low intensity farming. GEPARD predicts faunal richness and is based on multi-scaled resource-selection functions. Under both scenarios the area of predicted losses in species richness of birds and carabids was larger than the area of predicted gains in species richness. However, the area with predicted losses of avian richness was smaller under the direct income support scenario than under the production-based subsidy scenario, whereas the area with predicted losses of carabid species richness was smaller under the production-based subsidy scenario than under the direct income support. Yet locally, richness gains of up to four species were predicted for carabids under both scenarios. We conclude that the sometimes contrasting and heterogeneous responses of birds and carabids at different localities suggest the need for spatially targeted subsidy schemes. With the help of the GIS-based approach presented in this study, prediction maps on potential changes in local and regional species richness can be easily generated.