Farmland habitat diversity in marginal European landscapes changed significantly in the past decades. Further changes toward homogenization are expected, particularly in the course of European agricultural policy. Based on three alternative transfer payment schemes, we modeled spatially explicit potential effects on the farmland habitat diversity in a marginal European landscape. We defined (1) a scenario with direct transfer payments coupled to production, (2) a scenario with direct transfer payments decoupled from production, and (3) a scenario phasing out all direct transfer payments. We characterized habitat diversity with three indices: habitat richness, evenness, and rarity. The habitat pattern in 1995 served as reference for comparison. All scenarios predicted a general trend of homogenization of the farmland habitat pattern, yet to a differing extent. Transfer payments coupled to production (Scenario 1) favored the abandonment of agricultural production, particularly in low-productive areas and arable land use in more productive areas. Habitat richness and habitat evenness had intermediate values in this scenario. Decoupling transfer payments from production (Scenario 2) supported grassland as most profitable farming system. This led to a grassland-dominated landscape with low values of all habitat diversity indices. Phasing out transfer payments (Scenario 3) resulted in complete abandonment or afforestation of agricultural land and extremely low values in all habitat diversity indices. Scenario results indicate that transfer payments may prevent cessation of agricultural production, but may not counteract homogenization in marginal landscapes. Conserving high farmland habitat diversity in such landscapes may require support schemes, e.g., Pillar Two of EU Common Agricultural Policy.