Climate change is one of the largest threats for biodiversity as changing climatic conditions often make existing habitat sites less suitable. This poses new challenges for species conservation, in particular in agricultural landscapes, where climate change may also induce modifications in agricultural land use. To conserve species in agricultural landscapes, agri-environment schemes (AES) which compensate farmers for implementing conservation measures are commonly used. However, current research on the cost-effective design of AES largely ignores necessary adaptations of conservation measures given climate change. We develop a climate-ecological-economic (CEE) model to examine how the cost-effective design of AES has to be modified under climate change. We apply the model to the conservation of eight meadow bird species in Northern Germany and determine the cost-effective conservation measures under recent and future climatic conditions. We find that the timing of conservation measures in the AES needs to be changed in the RCP8.5 scenario given the species’ phenological adaptations and the impact of extreme events (inundations) on costs. The novelty of the research lies in the development of a CEE model which considers both spatial and temporal changes in costs and benefits to develop recommendations for the cost-effective design of AES under climate change.