Low available soil phosphorus (P) is associated with its immobility, which renders it unavailable for plant uptake. In addition, farmers normally apply inorganic fertilisers to legumes to activate soil-bound phosphorus using root exudates. Sufficient soil mineral nutrition is key to sustainable crop production, and hence food and nutritional security. The aim of this study was to quantify the acid and alkaline phosphatase activity as an indicator of P supply and availability under varying levels of nitrogen, phosphorus and potassium (NPK) fertilization and different cropping systems. An intercropping (cowpea and amaranth) and fertiliser (control, 25%, 50%, and 100% of the recommended NPK levels) field trial was laid out in a 2 × 4 factorial treatment structure in a completely randomized design (CRD) with four replications. There was higher acid and alkaline phosphatase activity in the rhizosphere of cowpea and amaranth grown as sole crops compared to those from intercropping. The cowpea and amaranth plants grown without fertiliser or 25% NPK had the highest rhizospheric phosphatase activity, while 100% NPK application exhibited the least. The markedly higher phosphatase activity from the low fertiliser application treatments indicates the possible stimulation of microbial activity to supplement P demands for the crops. The study revealed that the application of lower rates inorganic fertilisers in a legume intercrop stimulates the activity of the phosphatase enzymes, which can subsequently liberate soil-bound phosphorus. Plant tissue phosphorus concentration of cowpea and amaranth plants increased proportionately to the increase in fertiliser application up to 50% of the recommended NPK level. The land equivalent ratio (LER) was greater than 1, indicating that it is more beneficial to intercrop cowpea and amaranth as opposed to growing them as sole crops. Overall, the application of NPK fertilizer to amounts of up to 50%, based on the results of this study, appear to be better than 100% in terms of biomass accumulation and phosphate activity.