The indiscriminate use of chemical fertilizers can deteriorate soil, grain, and environmental quality; still, these can be restored if integrated nutrient management options with inclusion of legumes in the cropping system are adopted. A long-term (19 year) rice-wheat system experiment was examined to find out the best nutrient management practices (BNMP) through recommended dose of fertilizers (RDF), integrated plant nutrition system (IPNS), soil test crop response (STCR), farmyard manure (FYM), along with the inclusion of pulses (berseem and cowpea). Seven nutrient management practices were applied in combination of organic and chemical fertilizer in the rice-wheat system. Results showed that a significant variation was seen in phosphorus (P) fractions among the treatments and soil depths. The results showed a significantly (p < 0.05) higher contribution to phosphorus availability by Residual-P followed by NaHCO₃-Po > NaOH-Pi > NaOH-Po > HCl-P > NaHCO₃-Pi > available P and lowest in WSP under different long-term management options in rice-wheat system after completing 19 crop cycles. Variations in soil P-fractions with depth were compared to different treatment combination, and a considerable increase in all the major P-fractions was noticed. The continuous application of various IPNS options as organic farming (OF), RDF, STCR, and the inclusion of pulses (berseem and cowpea) significantly improved all P fractions in the soil system and offered an added benefit in terms of sustainability of production and soil health compared to the solo application of chemical fertilizers. Overall, results showed that IPNS options (berseem and cowpea) showed its superiority over the rest of the treatment. This study suggests that the inclusion of pulses would increase P-availability in soil system.