Soil microbes such as plant growth promoting rhizobacteria play significant roles in the solubilisation of inorganic phosphorus (P), mineralization of organic P and in improving plant P uptake. It is known that phosphate solubilising microorganisms (PSM) populations largely vary depending on the ecosystems, the cropping systems or the soil management. The capacity of Minjingu phosphate rock (PR) to enhance the populations of native PSM under three cereal–legume rotation systems was assessed in the third season of rotation. Triple super phosphate (TSP) was used as a positive control. In comparison to the negative control, application of Minjingu PR increased the total fungal diversity and phosphate solubilising bacteria (PSB) population by 67–90 % while high rates of TSP significantly (p < 0.05) reduced bacterial diversity and populations of PSB by 46–69 %. Minjingu PR also resulted in both crop and legume yields increase (41–104 % compared to the control), which were similar to those obtained with TSP application. Cropping systems incorporating sparingly soluble P sources such as Minjingu PR into soils can stimulate the populations of native PSB and agronomic productivity. They may represent a promising way of minimizing the utilization of mineral P fertilizers.