Many studies have explored farmers’ perspectives on biodiversity and ecosystem services, but fewer qualitative and cross-country comparisons exist. We develop a socio-ecological system to analyse agricultural landscape services, biodiversity, and drivers that have affected these services in recent decades. Via a systematic stakeholder mapping and 49 semi-structured interviews, we identify stakeholder perceptions of this system. We compare the perceptions across four regional case studies (Austria, Estonia, Germany, Switzerland), and two stakeholder groups (land managers and administrators). The case studies share certain commonalities in perceptions (e.g., provisioning and regulating services discussed in all of them) but also show differences (e.g., changes in biodiversity and landscape services more often perceived in the Swiss and German cases, but less in the Austrian and Estonian case studies). Across all case studies, typical land use change can be attributed to multiple drivers of various strengths, with climate change being the most often perceived driver directly affecting landscape services, followed by policies and market-based drivers, which affect services and biodiversity indirectly via land use. Compared to the administrators (e.g., decision-makers, scientists), the managers (e.g., farmers, NGOs) discuss more often the drivers, like various biodiversity and landscape service categories, as well as climate change, markets, and technologies. However, the administrators focus more on cultural services, policies as drivers, and consider more often links between drivers and landscape services and/or biodiversity. Hence, both of the groups’ (administrators and managers) perceptions partly complement each other. Since policy making should be based on the best knowledge of different stakeholder groups, active knowledge exchange between managers and administrators should be supported and outcome considered in decision making. The resulting regional differences in stakeholder perceptions of the drivers and their respective impact on agricultural landscapes suggest that future agricultural policies need regional targeting and the consideration of landscape-specific characteristics.