Abstract: The ongoing trend toward agricultural intensification in Southern Amazonia makes it essential to explore the future impacts of this development on the extent of natural habitats and biodiversity. This type of analysis requires information on future pathways of land-use and land-cover change (LULCC) under different socio-economic conditions and policy settings. For this purpose, the spatially explicit land-use change model LandSHIFT was applied to calculate a set of high-resolution land-use change scenarios for the Brazilian states Para and Mato Grosso. The period of the analysis were the years 2010–2030. The resulting land-use maps were combined with maps depicting vertebrate species diversity in order to examine the impact of natural habitat loss on species ranges as well as the overall LULCC-induced effect on vertebrate diversity as expressed by the Biodiversity Intactness Index (BII). The results of this study indicate a general decrease in biodiversity intactness in all investigated scenarios. However, agricultural intensification combined with diversified environmental protection policies show least impact of LULCC on vertebrate species richness and conservation of natural habitats compared to scenarios with low agricultural intensification or scenarios with less effective conservation policies.