Integrated land use models (ILM) are increasingly applied tools for the joint assessment of complex economic-environmental farming system interactions. We present an ILM that consists of the crop rotation model CropRota, the bio-physical process model EPIC, and the farm optimization model FAMOS[space]. The ILM is applied to analyze agri-environmental measures to maintain biodiversity in an Austrian landscape. We jointly consider the biodiversity effects of land use intensity (i.e. nitrogen application rates and mowing frequencies) and landscape development (e.g. provision of landscape elements) using a rich indicator set and region specific species-area relationships. The cost-effectiveness of agri-environmental measures in attaining alternative biodiversity targets is assessed by scenario analysis. The model results show the negative relationships between biodiversity maintenance and gross margins per ha. The absence of agri-environmental measures likely leads to a loss of semi-natural landscape elements such as orchard meadows and hedges as well as to farmland intensifications. The results are also relevant for external cost estimates. However, further methodologies need to be developed that can jointly and endogenously consider the complexities of the socio-economic land use system at farm and regional levels as well as the surrounding natural processes at sufficient detail for biodiversity assessments.