Rice, the predominant food crop in India, is being grown traditionally with improper plant nutrient management mostly under the flooded situation. Recent advancement in research on crop science focuses on water-saving rice technologies for maximization in crop and water productivity under the backdrop of a shrinking water resource base for ensuring environmental and agricultural sustainability. Under this situation, an experiment was conducted in two consecutive years in a split-plot design keeping rice cultivation methodologies, viz., aerobic culture, System of Rice Intensification (SRI), and conventional flooded culture in main plots and integrated plant nutrient management (INM) treatments in sub-plots. The experiment was aimed at understanding the effects of different rice production systems and INM on nutrient content, uptake, and use efficiency. The change in soil quality parameters was also studied to understand the impact of crop establishment methods (CEM) and INM options. Significant reduction (p ≤ 0.05) in nutrient uptake and use efficiency was observed under aerobic culture compared to SRI and flooded method, although aerobic culture showed the highest physiological nitrogen use efficiency. Post-harvest available Fe status was significantly lower in aerobic rice (mean 10.39 ppm) compared to other crop establishment technologies; however, Zn status was higher in aerobic rice over the flooded situation. Although available potassium was not affected due to rice cultivation methods, available nitrogen and phosphorus status were influenced remarkably. Soil microbial quality was improved in aerobic rice in comparison to flooded rice. SRI proved to be the most efficient rice establishment method for enhancement in nutrient uptake, use efficiency, and enrichment of soil chemical and microbiological quality. Irrespective of crop culture, integrated plant nutrition in rice improved the nutrient uptake, use efficiency, and soil quality parameters. The study revealed that, under the alluvial soils of the Indo-Gangetic Plains of Eastern India, SRI can be considered as a water-saving rice production method. The method can also improve nutrient uptake, efficiency, and soil quality parameters if proper INM is adopted.