Identifying appropriate nutrient management options is crucial for reversing the yield plateau and enhancing the nutritional status of basmati rice under the basmati rice-wheat cropping system of the Indo Gangetic Plain (IGP). Alternative to the conventional chemical fertilizer, ZnO nanoparticles as carrier material for the micronutrient Zn has shown promise in reducing the bulkiness of fertilizer use in the soil–plant environment. But whether its integration and interaction with an organic source such as green manuring could enrich basmati rice grain with micronutrients and promote protein nutrition is not well investigated. Therefore, we conducted a field experiment during the summer and rainy seasons (April–October) of 2020 and 2021 at the research farm of the ICAR-Indian Agricultural Research Institute, New Delhi in a split-plot design with two summer green manuring (SGM) options (Sesbania and cowpea, along with fallow) as main plots and six fertilization strategies as subplots: 5 kg Zn ha−1 as bulk ZnO, N at 120 kg N ha−1 as prilled urea (PU), N at 120 kg N ha−1 as PU + 5 kg Zn ha−1 as bulk ZnO, 1% bulk ZnO-coated PU, 0.1% nano ZnO coated PU and 0.2% nano ZnO coated PU replicated thrice. On average, SGM increased basmati rice grain yield by 13.2 and 12.3% during 2020 and 2021, respectively compared to fallow. Integrated application of zinc with urea significantly (p < 0.05) increased the grain yield of basmati rice by 9.56% and by 10.5% relative to urea without zinc and by 33.7 and 33.8% than the sole application of 5 kg Zn ha−1 through ZnO, respectively during 2020 and 2021. On average, SGM boosted Zn, Cu, Mn, and Fe content in milled rice by 25, 22.38, 20.0, and 18.85% during 2020 and 23.75, 21.4, 19.6, and 13.3% during 2021, respectively compared to fallow. Relative to sole urea application, zinc, and urea together improved the Zn and Fe content in milled rice by 2.99 mg kg−1 and 2.62 mg kg–1, respectively during the first year and by 2.83 mg kg−1 and 2.6 mg kg−1, respectively during the second year of study. The highest protein content in basmati rice grain was observed when it was grown after Sesbania aculeata residue incorporated plot during both the years and it decreased in the order: Sesbania aculeata > Vigna unguiculata > summer fallow. Our findings revealed that with the application of 1% bulk ZnO coated PU with Sesbania; the yield response, micronutrient acquisition, and protein accumulation in milled rice was higher than in other plant fertilization methods. However, in plots treated with Sesbania, along with 0.2% nano ZnO-coated PU exhibited statistically equivalent yield and micronutrient loading in edible tissues. Hence, this study unveils the critical role of nano ZnO-coated urea and summer green manuring in elevating micronutrient and protein bioavailability in basmati rice and concurrently reducing Zn dose by 20%, making it a profitable option for farmers.