Current production systems for crops, meat, dairy and bioenergy in the European Union (EU) rely strongly on the external input of nitrogen (N). These systems show a high productivity per unit of land. However, the drawback is a complex web of N pollution problems contributing in a major way to degradation of ecosystems. European Union Directives and national policies have improved nutrient management and reduced fertilizer N use in most European countries, which has curbed the N pollution trends particularly in regions with high stocking rates of animals. However, improvement is slowing down and environmental targets for N are not within reach. Building on the 2011 European Nitrogen Assessment, the current paper reviews key features of the complex relationships between N use and food production in Europe in order to develop novel options for a more N-efficient, less N-polluting and secure European food system. One option is to relocate feed and livestock production from Northwestern to Central and Eastern Europe. This would allow a reduction of N rates and N pollution in cereal production in Northwest Europe by 30% (50 kg N/ha), while increasing total cereal production in Europe. Another option is a change towards legume-based cropping systems to produce animal feed, in order to decrease dependence on N fertilizer and feed imports. The greatest challenge for Europe is to decrease the demand for feed commodities, and thus for land and N, by a shift to more balanced (and healthier) diets with less animal protein. These drastic changes can be stimulated by targeted public–private research funding, while the actual implementation can be enhanced by smart payment schemes using, for example money from the Common Agricultural Policy, certification and agreements between stakeholders and players in the food and energy chain. Involving networks of consumers, producers and non-governmental organizations is critical. An effective strategy starts with convincing consumers with a Western diet to eat less meat and dairy by communicating the associated health benefits and smaller ecological footprints. Internalizing the cost of N pollution leading to increased prices for N-intensive food products may also enhance involvement of consumers and provide financial resources to compensate farmers for loss of income and extra costs for stricter N measures.