Soil organic matter (SOM) is a highly complex variable and needs fractionation into distinct pools based on their differing behaviour to better elucidate and predict its dynamics. The present study aimed to quantify the soil organic carbon (SOC) and total nitrogen (TN) stocks and assess their sensitivity indices in fractions with contrasting functionality. Furthermore, the correlations were also evaluated between SOC and TN stocks of pools, system grain yield (SGY), soil physico-chemical properties, and climatic variables. The results demonstrated that C and N stocks in the combined application of organic manure (M), and nitrogen, phosphorus, and potassium (NPK) i.e., MNPK and sole application of M treatments significantly augmented at 0-40 cm and 40-100 cm soil layers, respectively. Also, the SGY was significantly higher under all fertilization treatments than control (no fertilization). Furthermore, SOC and TN stocks of major soil fractions were positively correlated with soil nutrients and mean annual precipitation. Thus, long-term manure application integrated with mineral fertilization (MNPK) in Black soil or Mollisol leads to enhanced crop yields and pool-associated SOC and TN stocks up to 40 cm depth. Whereas the manure-alone (M) is critical for enhancing pool-associated SOC and TN stocks at 40 to 100 cm soil profile. This study implicated how the SOC and TN stocks in different fractions respond to manure and mineral fertilization (35 years) which is pivotal for improving SOC and TN sequestration by modulating the response of SOM pools. The results provide insights into the accrual of C and N stocks underpinned by the stabilization mechanisms specifically implying the significance of microaggregation across the soil profile of cropland.