Nutrient-poor soils coupled with micronutrient deficiency among many rural resource-poor communities remain a challenge in sub-Saharan Africa. Nutrient-poor soils can be managed through various soil amendment or fertilisation strategies. Micronutrients can be supplied through plants. The study was aimed at determining the symbiotic nitrogen fixation of cowpea as well as the contribution of inter-cropping under varying levels of nitrogen, phosphorus, and potassium (NPK) fertilisation. In addition, the amount of micronutrients supplied by cowpea and amaranth were determined. The experiment was laid out in a 2 × 4 factorial treatment structure in a completely randomised design, with inter-cropping (cowpea and amaranth) and fertiliser (control, 25%, 50%, and 100% of the recommended NPK levels) as treatment factors with four replications. Symbiotic N2 fixation of cowpea decreased from 341–448 kgN.ha−1 to 77–91 kgN.ha−1 for the first year and 557–227 kgN.ha−1 to 92−164 kgN.ha−1 for the second year with fertilisation. The iron and zinc nutritional yield increased (61–210 g.ha−1 for first year and 304–867 g.ha−1, for second year), proportional to fertiliser application to both crops. The research shows the benefits of leguminous crops in soil nutrient fertility and inorganic fertilisation with inter-cropping in managing micronutrient deficiency to meet the nutritional needs of rural communities.