Agricultural intensification is a major driver of biodiversity decline throughout Europe. Agri-environment schemes governed by EU regulation are a significant tool in combating this decline but despite high spending, experiences of their effectiveness have been mixed. Their effectiveness might be improved by targeting them to locations with high biodiversity value, and particularly by spatial coordination to enhance habitat connectivity and the associated ecological processes, such as dispersal. We show, with an example of semi-natural grassland conservation in South-Western Finland, how spatial conservation planning tools, here the Zonation software, could help in assessing the habitat connectivity and allocating management actions. We assign highest priority to sites that have been classified as nationally important and that have been under management, and let connectivity influence the Zonation prioritizations. According to Zonation outputs, 25–30% of highest-ranking grasslands in our study area are without management contracts, indicating weak connectivity of managed sites, whereas Natura 2000 areas are spatially better located. A 50% expansion of the current network would be adequate to bring its value close to that of a network created from scratch, but as the contracts are temporary, reallocation of the contracts from the least valuable, funded sites to more valuable, unfunded ones would be even more effective. Current policy instruments supporting farmland biodiversity are strongly constrained by EU regulation, and appear to be too inflexible to take the spatial differences in conservation values into account. Better communication and incentives to encourage farmer participation to these voluntary programs are needed.