To prevent further biodiversity loss as a result of intensive agricultural practices, Agri-Environmental Schemes (AES) have been implemented on European farmland. Unfortunately these AES have not always been effective in terms of biodiversity and farmer participation. In an effort to improve the AES programme the Dutch government switched from an individual application system to a collective application system for AES payments in 2016. The goal of this paper is to analyse how the resilience of the land use system in terms of farmer participation in the AES and biodiversity is affected by the value farmers attach to biodiversity, and whether the shift from an individual to collective AES will affect the resilience of the land use system. We constructed a multi-objective mathematical programming model in which farmers maximise utility. Farmers are linked through their common effect on biodiversity. In the collective application system payments are only available when the biodiversity in the region is above a certain threshold. Simulation results show no difference in farmer participation and biodiversity between the individual application system and the collective application system when biodiversity weights are high. The land use system loses its resilience in terms farmer participation in the AES and biodiversity if we lower the biodiversity weights, this effect is stronger in the collective AES programme.