Pearl millet (Pennisetum glaucum [L.] R. Br.) is a climate-smart cereal crop for environments prone to drought and heat stresses. Pearl millet is cultivated in Pakistan on marginal soils with phosphorus (P) deficiency, which significantly decreases its productivity. Moreover, P fixation in the country’s calcareous soils is another major constraint which requires attention. P solubilizing bacteria (PSB) have the potential to improve P availability in the soil. However, the potential of PSB in improving P availability in soil and pearl millet yield has been rarely tested in Pakistan. Therefore, this 2-year field study explored the role of combined application of organic and inorganic P sources along with PSB (i.e., Bacillus sp. MN54) inoculation to improve yield-related traits, P use efficiency (PUE), net economic returns and grain quality of pearl millet grown under semi-arid climatic conditions. Phosphorus was applied through inorganic sources, organic sources (farmyard manure) and 50% inorganic sources + 50% organic sources with or without PSB inoculation. In control treatment, pearl millet was grown without P application. The individual and combined application of P from different sources and PSB inoculation significantly improved yield-related traits and PUE of pearl millet. The highest grain yield was observed with combined (50% inorganic + 50% organic) application of P with PSB inoculation. The same treatments resulted in higher iron, zinc, protein and P contents in the grains during both years. Likewise, P application through organic and inorganic sources combined with PSB inoculation improved soil bulk density, fertility and microbial population during both years. The highest economic returns and benefit–cost ratio was recorded for combined P application (50% inorganic + 50% organic) and PSB inoculation. In crux, the combined application of organic and inorganic P fertilizers along with PSB (Bacillus sp. MN54) inoculation seemed a feasible approach to enhance productivity, grain quality and net economic returns of pearl millet. Therefore, it is recommended that P should be applied through both organic and inorganic sources combined with PSB inoculation to improve P availability and productivity of pearl millet in Pakistan. The current study has explored the potential of combined P application through organic and inorganic sources along with PSB inoculation. Future studies should focus on the determination of mobilized P with the application of PSB.