The sustainability of crop production systems depends on the adoption of practices that allow the balancing of nutrient output and the preservation of soil organic matter. In Brazil, no-tillage (NT) is widely adopted for soybean-based cropping systems. In the Southern region, soybean alternates with maize in the summer and black-oats or wheat in the winter. Green-manure legumes are occasionally introduced in the crop rotation to break the continuous use of wheat in the winter. The objective of the present study was to evaluate if NT adoption would increase biological nitrogen fixation to soybean and other legumes. The hypothesis that a system richer in N would bring about positive effects on soil C stocks, was also tested. The study was carried out in Londrina, Paraná State, in Southern Brazil on a clayey Ferralsol that was cropped under NT with soybean as the main crop for more than 25 years. In 1997, three different crop rotations under both NT and conventional plough tillage (CT) were introduced. The crop rotations were composed of soybean, maize, wheat, black-oats and white lupins, but differed from each other in the frequency that each crop appeared in the rotation. Crop yields and the biomass of lupins and black-oats were quantified at every harvest during the 12 years of this study. Conversion factors of measured yield and biomass into C and biologically fixed N inputs to the crop system were developed from whole plant measurements performed in four of the twelve years of the study. The contribution of biological N2 fixation (BNF) to the legumes was determined using the ureide abundance and the 15N natural abundance techniques in 1998, 1999, 2005 and 2007. From these data, the calculation of N balance for each rotation (input N minus output N in harvested grain) was carried out. Soil C and N stocks to 80cm depth were quantified in 1997, 2003 and 2009. Grain yields were higher under NT for soybean and under CT for maize, in the rotation with the lowest frequency of legume crops. Soybean reliance on BNF was higher under NT (76%) than under CT (68%) whilst for lupins the reliance was 68% under NT and 60% under CT. The use of lupins as a green manure represented an extra contribution to soil N of approximately 300kgNha−1 and this was essential to maintain a positive N balance for the system. The comparison of soil C stocks between 1997 and 2009 revealed almost no gain in soil C under NT, but a C loss of 19MgCha−1 after 12 years of CT. Significant soil C and N losses were recorded in the rotation where lupins were planted more frequently and fertilizer N application to maize was suspended, which resulted in a very negative N balance for the system. The results highlight the importance of NT to enhance BNF inputs to the system and the need to recognize the N balance as a key driver of C stock changes in the soil. In addition, it suggests NT in this study had the consequence of avoiding soil C loss rather than increasing soil C stocks.