The public promotion of renewable energies is expected to increase the number of biogas plants and stimulate energy crops cultivation (e.g. maize) in Germany. In order to assess the indirect effects of the resulting land-use changes on biodiversity, we developed six land-use scenarios and simulated the responses of six farmland wildlife species with the spatially explicit agent-based model system ALMaSS. The scenarios differed in composition and spatial configuration of arable crops. We implemented scenarios where maize for energy production replaced 15% and 30% of the area covered by other cash crops. Biogas maize farms were either randomly distributed or located within small or large aggregation clusters. The animal species investigated were skylark (Alauda arvensis), grey partridge (Perdix perdix), European brown hare (Lepus europaeus), field vole (Microtus agrestis), a linyphiid spider (Erigone atra) and a carabid beetle (Bembidion lampros). The changes in crop composition had a negative effect on the population sizes of skylark, partridge and hare and a positive effect on the population sizes of spider and beetle and no effect on the population size of vole. An aggregated cultivation of maize amplified these effects for skylark. Species responses to changes in the crop composition were consistent across three differently structured landscapes. Our work suggests that with the compliance to some recommendations, negative effects of biogas-related land-use change on the populations of the six representative farmland species can largely be avoided.