Optimization of the nitrogen (N) inputs and minimization of nutrient losses strongly affect yields in crop rotations. The aim of this research was to evaluate the effect of agricultural practices on yield and N use in a 4-year cereal-legume rotation in organic farming and to identify the best combination of these practices. The following treatments were compared: conventional plough (P) vs. reduced chisel (RC) tillage; composted farmyard manure (F) vs. unfertilized control (NF); and green manure (GM) vs. no green manure (NoM). No significant differences were found for N use efficiency between P and RC in each crop. The results suggested that legumes in the tested rotation do not need supplemental N fertilization, particularly if combining GM and F. The use of composted farmyard manure should be considered in a long-term fertilization plan for cereals, to allow a higher efficiency in N use. The residual effect of fertilization over time, along with the site-specific pedo-climatic conditions, should also be considered. In both tested tillage approaches, soil N surplus was the highest in plots combining GM and F (i.e., more than 680 kg N hað€€€1 in combination with RC vs. about 140 kg N hað€€€1 for RC without fertilization), with a risk of N losses by leaching. The N deficit in NoM-NF both combined with P and RC would indicate that these treatment combinations are not sustainable for the utilized crops in the field experiment. Therefore, the combination of the tested practices should be carefully assessed to sustain soil fertility and crop production.