Agri-environmental schemes (AES) aimed at promoting farmland biodiversity are a key agricultural policy instrument in Switzerland. While the share of farmland managed under AES has expanded, traditional orchard meadows, regarded as agrobiodiversity hotspots, are declining. It is not clear yet what role AES play in maintaining orchard meadows, considering the effects of different farm management. Thus, the objective of this study was to examine the effects of AES on farmers’ decision-making regarding orchard meadows across a range of farm types. We developed an ecological-economic assessment model by integrating the results of the expert system SALCA-BD (Swiss Agricultural Life Cycle Assessment—Biodiversity) into the optimization-based bio-economic farm model (BEFM). We applied the model to five typical farm types (small dairy, large dairy, suckler, orchard, and small farms) identified in a rural region of northern Switzerland. Modeling results show that the adoption of AES considerably varies among farm types according to the compliance cost of participating in AES. Also, the current AES do not provide farmers with sufficient payments to maintain any type of orchard meadows. Instead, converting orchard meadows into arable land would generate higher incomes for farmers. This study recommends farm type specific payments to different farm types and a regulatory framework that incentivizes farmers to preserve the existing area of orchard meadows.