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Eutrophication caused by agriculture is an increasing ecological threat to the Baltic Sea. Modern, resource-efficient farming systems based on integrated plant and animal production, effective nutrient recycling and low external inputs can enhance multiple agro-ecosystem services, resulting in reduced pollution. Practical examples of such farming systems are not widespread. Therefore, the Baltic Ecological Recycling Agriculture and Society (BERAS) Implementation project aimed to foster this systemic shift. In this paper, agronomic strategies are described to improve nitrogen (N) efficiency for the conversion to ecological recycling agriculture (ERA). First, N farm gate balances of 22 farms in conversion are presented. They showed a large variation from −9 to 90 kg∙N∙ha−1∙a−1. Then, the use of guidelines and advisory tools to improve the nitrogen efficiency is described. The legume estimation trainer and nitrogen budget calculator help assess and optimize the nitrogen supply from legumes under farming conditions. The application of the crop rotation planning tool “ROTOR” guides advisors and farmers to identify agronomically and environmentally sound rotations. The tools can help overcome key agronomic constraints by implementing ERA. The necessity of accompanying measures from policy and the need to change food consumption patterns are discussed.