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Increasing food production without further harming biodiversity is a key challenge of contemporary societies. In this paper, we assess trade-offs between agricultural output and two key agri-environmental indicators in four contrasting scenarios for Europe in 2040. The scenarios represent different storylines encompassing assumptions on macro-economic drivers (e.g. population and GDP growth rate), demand for food and livestock products as well as policy choices on trade liberalisation/protectionism, biodiversity conservation, regulations on land-use planning and subsidies to farmers through the European Union (EU) Common Agricultural Policy (CAP). Through a complex modelling chain, we projected for the year 2040: i) the total energy content of agricultural output; ii) the total nitrogen surplus, a proxy of the overall impact of agriculture on the environment; and iii) an index measuring the capacity of agricultural systems to support biodiversity. We present both aggregate results (EU level) and spatially explicit assessments at a fine resolution (1 km(2)). Results indicate that a strong neo-liberal approach to agriculture (full liberalisation, abolition of subsides) will lead to increased use-input efficiency and decrease of impact from Nitrogen input; however, a large amount of agricultural area in Europe will be abandoned, which will lead to an absolute decrease in production and increased land homogenisation and polarisation, with negative effects on the capacity of agricultural areas to support biodiversity. Protectionist and sovereigntist policies will keep absolute production and cultivated area high, but at the cost of less efficiency in the use of inputs and higher impacts on the environment and biodiversity. Under a scenario characterised by environmental-friendly practices, multifunctional landscapes and localism, significant decreases in the environmental pressure of agriculture (compared to other scenarios) can be achieved with minimum decrease in agricultural output. Our results indicate that agricultural and land-use policies aiming at preserving production over large rural areas, multifunctionality and diversification of agricultural landscapes can contribute to the jointly achievement of biodiversity protection and high food production.