<p>Long-term monitoring of soil properties is essential for assessing the sustainability of nutrient management practices affecting soil fertility and crop productivity. Effective fertilizer management is crucial in the rice–wheat system, particularly in the Indo-Gangetic Plain, a key food security and environmental sustainability region. A 22-year study evaluated the impact of balanced fertilization using inorganic fertilizers alone and in combination with organic amendments, including farmyard manure (FYM), rice straw incorporation (SI), and green manure. The application of chemical fertilizers alone or with organic manures significantly increased N, P, and K levels by 37–65%, 74–142%, and 56–85%, respectively, compared to the unfertilized control. Soil organic carbon (SOC) rise from 2.42&#xa0;g&#xa0;kg⁻¹ in 1999 to 5.45&#xa0;g&#xa0;kg⁻¹, while bulk density declined from 1.49&#xa0;Mg&#xa0;m⁻³ to 1.38&#xa0;Mg&#xa0;m⁻³ by the application of NPK fertilizers in combination with organic manures. Fertilization treatments notably increased very labile carbon (97–174%) and labile carbon (74–103%) compared to the control. Similarly, plots that received organic and inorganic fertilizers exhibited higher levels of less-labile and non-labile carbon contents, with increases ranging from 34 to 72% and 63 to 77%, respectively, in comparison to the control. Among treatments, 100% NPK + FYM recorded the highest carbon management index and lability index, followed by 100% NPK + SI. The highest rice (7.65 t ha⁻¹) and wheat (5.89 t ha⁻¹) yields were also achieved with 100% NPK + FYM. Long-term fertilization strategies significantly impact nutrient uptake and efficiency, with integrated approaches like 50% NPK + FYM demonstrating superior agronomic performance in both rice and wheat. In conclusion, the combined application of 100% NPK and FYM significantly enhanced SOC, improved soil fertility, and increased crop productivity in the rice–wheat system.</p>