What nutrient supply options can ensure maximum productivity and optimize the nutrient uptake of rice–wheat system (R-W system)? an experiment started in the year 1998 (19-year-old) to examine the impact of optimal nutrient supply (NS) strategies to maximize crop productivity and nutritional security in R-W system. To determine the best nutrient management strategies (BNMS), seven different NS methods were tested. These included (organic and mineral fertilizers), as well as combinations such as integrated plant nutrition system (IPNS), IPNS + B (berseem), and IPNS + C (cowpea), with the aim of enhancing the productivity and nutrient absorption of R-W system. Results showed that rice grain yield notably wide-ranging from 1.61 to 5.81 t ha−1 under different NS options and highest rice grain yield (mean of 19 years) was observed at IPNS + C (5.81 t ha−1), which was at par with IPNS (5.79 t ha−1), STCR (soil test crop response) (5.76 t ha−1) and IPNS + B (5.67 t ha−1) followed by 100% recommended dose fertilizer NPK (4.41 t ha−1), which equality with OF (organic farming) (4.04 t ha−1) and lowest was recorded in control plot (1.61 t ha−1). Wheat grain yield varied significantly from 1.43 to 5.86 t ha−1 under different NS options. The highest yield (mean of 19 years) was observed in treatments IPNS + B (5.86 t ha−1), IPNS (5.77 t ha−1), IPNS + C (5.48 t ha−1), and STCR (5.45 t ha−1), followed by OF at 4.49 t ha−1, NPK at 3.76 t ha−1, with the lowest in the control plot at 1.43 t ha−1. Additionally, total phosphorus and sulfur accumulation in rice (grain: 8.41 to 39.09 kg ha−1; straw: 6.02 to 23.54 kg ha−1) varied significantly across nutrient supply treatments. Overall, adoption of IPNS integration with legumes (IPNS + B and IPNS + C), can significantly improve productivity and nutrient accumulation in R-W systems. Incorporating legumes into farming practices is advised for sustained productivity and nutritional benefits.