Low yield of staple crops such as maize sorghum, pearl millet, and legumes in southern Africa poses a threat to food security, especially in the semi-arid regions of Botswana. The low crop productivity is caused by pests, low fertility, low soil moisture, and high temperatures possibly resulting from climate change. On-farm measurements of N2 fixation were done in groundnut and Bambara groundnut. Bacteria isolated from their root nodules were assessed as inoculant for cereals under greenhouse conditions. We also determined the most effective sorghum intercrop for reducing yield losses of sorghum caused by stem borers. The results showed that grain legumes fixed N2 under on-farm conditions. However, amounts of N-fixed on farmers’ fields were low because of suboptimal plant densities. Bambara groundnut growing in Lekobeng in Tswapong area fixed the highest amount of nitrogen at 1.3 kg N/ha, a value that is low because of the low planting density used by farmers. Bacteria isolated from legumes showed potential as biofertilisers. For example, in a clayey soil, there were no differences in the number of millet leaves between inoculated and NPK-fed plants. Finally, intercropping of sorghum with legumes led to a reduction in stemborer infestation on sorghum, resulting in higher grain yields for intercrops, about 8.4x more than monocropped sorghum. Taken together, these results show the potential use for legumes and their associated bacteria as biofertilisers in sustainable cropping systems. The data on intercropping will be used to advise farmers on the importance of legume intercrops in controlling stemborers.