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Phosphorus and zinc are important nutrient elements of concern in upland rice production. To determine the suitable combination of phosphorus, nanoparticles (NPs), and bio-fertilizer application as an alternative nutrient management approach in upland rice cultivation, a Polyvinyl Chloride (PVC) column experiment was conducted under controlled conditions in 2015. The treatments consisted of three phosphorus levels, two foliar sprays of NPs (ZnO and TiO2), and PSB seed treatment. The results indicated that the combined application of P (50 kg ha−1), ZnO NPs (500 ppm), and PSB seed treatment (20 g kg−1) improved the root system architecture traits of rice (total root length: 3.73–6.74%, diameter: 8.57–22.22%, and volume: 3.40–3.70%) at depths of 0–30 cm and 30–60 cm, compared to higher P + TiO2 NPs + no PSB. Consequently, this combination led to an enhancement in photosynthetic leaf area (by 3.3%), tiller numbers (by 7%), and dry matter production (by 35.5%). The favorable root growth resulting from the application of higher P and PSB enhanced zinc uptake by rice grains (by 38.44%) and straw (by 26.99%). Furthermore, the supplemental application of PSB improved the activity of soil enzymes such as dehydrogenase and phosphatase. As a result, maximum phosphorus use efficiency (PUE; 31.5%) was achieved through the combined application of P (50 kg ha−1) × ZnO NPs × PSB. In conclusion, this study demonstrated the beneficial effects of an integrated approach involving phosphorus, PSB, and metal oxides (ZnO NPs) as a fertilizer management strategy to enhance the total biomass and PUE of upland rice. [ABSTRACT FROM AUTHOR]