Agroecosystems represent 38 % of global land use. Agroecosystems are located close to human settlements and are managed to produce food and fibers, traded in markets. Agroecosystems also produce other goods and services essential to human beings, such as climate regulation, flood mitigation, and landscape amenity. Economists and ecologists have developed the ecosystem services framework to foster the provision of these non-commercial services. Scientists can therefore help decision makers to develop sustainable ecosystems by studying ecosystem services. Here, we analyze the trade-offs of ecosystem services of farming systems. We discuss case studies of mixed perennial crops. The set of ecosystem services provided by these agroecosystems depends on their composition, structure, and management. Complex rule-based management will be required if winegrowers are to maintain an adequate set of ecosystem services across contrasting climatic years. Innovations including cover crops in banana systems can fulfill most of the objective set but will rely on increased farm labor. We then discuss the advantages, challenges, and opportunities to include the description of relations between ecosystem services in cropping system design. We propose to extend the yield gap analysis to ecosystem services, as a service gap analysis. This extension faces methodological questions about the potential provision of a service in a region. We conclude on the challenges that need to be faced if we want to use ecosystem services trade-offs to improve the contribution of agricultural systems to human well-being.