Context: Soil organic carbon (SOC) plays a critical role in maintaining soil fertility, structure, and resilience, especially under intensive production systems. However, long-term data on the role of integrated nutrient management (INM) practices in SOC stabilization and COQ-sequestration remains limited in semi-arid regions of India Objective: This study aimed to evaluate the long-term effect of balanced fertilization using farmyard manure (FYM) and inorganic fertilizers on SOC pools, soil health, and COQ-sequestration under the pearl millet-mustard-cowpea (PM-Mu-C) production systems. Methods: A long-term field experiment (initiated in 1980 and modified in 1994) was conducted on loamy sand soil at Anand Agricultural University, Gujarat, India. The study tested eight treatments involving varying FYM (0 and 10 t ha-1) and nitrogen-phosphorus (NP) fertilizer levels (0%, 50%, 100%, and 150% of the recommended dose). Soil samples were collected from 0 to 15 cm and 15-30 cm depths after summer cowpea harvest in 2023 and analyzed for SOC pools, microbial activity, and nutrient availability. Results: Application of FYM at 10 t ha-1 combined with 150% NP fertilizer significantly enhanced total organic carbon by up to 31.9% in surface soil (0-15 cm) and 18.3% in sub-surface (15-30 cm). Active and passive carbon pools increased substantially (40-193.6%), accompanied by a marked rise in microbial biomass carbon (46.7-49.8%). The SOC stock improved by 9.2% over five years, and COQ-sequestration rates reached 0.22 and 0.23 Mg C ha-1 yr-1 in 0-15 cm and 15-30 cm depths, respectively, representing increases of 266.7% and 130.0% over control. Soil bulk density decreased by up to 3.27%, while porosity and water holding capacity increased by 4.2% and 13.7%, respectively. Conclusions: Long-term application of FYM (10 t ha-1) and higher NP (150%) fertilizer doses substantially improves SOC dynamics, nutrient availability, and microbial activity in the PM-Mu-C production systems. Implications and limitations: This study highlights the potential of integrating organic and inorganic nutrient sources to enhance COQ-sequestration and maintain soil health in intensive production systems. Adoption of FYM at 10 t ha-1 with 150% NP fertilizer is recommended as a sustainable practice for improving soil resilience and mitigating climate change impacts in field crop systems