European farming systems are diverse, and food has traditionally played a central role in the shaping of individual and cultural identities. In this chapter, taking a food systems approach, we examine European issues for the interrelationships among agriculture, environmental sustainability, nutrition, and health, considering all steps in the food value chain from growing through to consumption and recycling. There are multiple policy objectives and instruments to coordinate, but, although the challenges are unprecedented, so too are the scientific opportunities. A wide range of issues are covered, including those for: agroecology and the implications for ecosystem assessment, other new production systems, linking soil structure and health both with environmental sustainability and novel products of the bioeconomy, and microbiomics. There are major opportunities for developing climate-resilient food systems while, at the same time, reducing the contribution that agriculture makes to climate change, along with accompanying implications for food policy. Recommendations for ambitious action include: promoting transdisciplinary research to fill present knowledge gaps; continuing to strengthen the research enterprise in the EU, recognising that EU scientists have crucial roles to play in building global critical mass in food system science; and reaffirming the use of science to inform innovation, policy and practice. In particular, for the EU, the Farm-to-Fork (F2F) policy has important objectives, but must be fully informed by the scientific evidence, well aligned with biodiversity, the circular economy and bioeconomic strategies, and transparent in communicating the consequences both for the domestic consumer and for the rest of the world.