Soybean production can contribute to the nitrogen economy of smallholder farming systems, but our understanding of factors explaining variability in nitrogen fixation and rotational benefits across farms and regions is limited. Biological nitrogen fixation (BNF) was quantified with the natural abundance method in 150 farmer-managed soybean plots under different varieties and inputs in Dowa, Mchinji and Salima districts of Malawi. Soybean yielded on average 1.2tha-1 grain and the above-ground biomass at mid pod filling (R5.5) was 2.8tha-1 and contained in total 63kgha-1 nitrogen derived from the atmosphere (Ndfa). Locally sourced varieties obtained a larger %Ndfa (65%) than the 'improved' variety Nasoko (53%). The %Ndfa was positively associated with soil sand content, sowing date, plant population and biomass accumulation, but it was not affected by inoculation with rhizobia or the combination of inoculation and NPK fertiliser application. Quantities of N2 fixed differed between regions and years, and was enhanced by applying inoculant and fertiliser together, leading to more biomass accumulation and larger grain yields. Soil available P and exchangeable K contents also increased the total amount of N2 fixed. In a related trial, continuous maize yields were compared with maize following soybean in 53 farmer-managed fields. Average yield in continuous maize was 2.5tha-1, while maize after soybean produced 3.5tha-1 (139% of continuous maize). Farmers with higher maize yields, who applied external nutrient inputs, and with a larger value of household assets achieved greater yield responses to rotation with soybean. A relative yield increase of more than 10% was observed on 59, 90 and 77% of the fields in Dowa, Mchinji and Salima respectively. We conclude that fields of soybean and maize that receive adequate nutrient inputs and good management to ensure good yields benefit most in terms of quantities of N2 fixed by the legume and the yield response of the following maize crop. The results suggest that the promotion of soybean-maize rotations should be done through an integrated approach including the promotion of appropriate soil and crop management techniques. Furthermore, they suggest that wealthier households are more likely to apply adequate nutrient inputs and good crop management practices and are likely to receive larger maize yield responses to the incorporation of soybean.