Degradation of soil quality caused by conventional tillage practices is a major concern for the sustainability of rice-wheat cropping systems in South Asian region. Therefore, suitable conservation agriculture (CA) practices are required. This study investigates the stratification and storage of soil organic carbon (SOC) and total nitrogen (TN) as affected by eight years of different CA practices in the North-West Indo-Gangetic Plains of India. There were four treatments: (1) conventionally tilled rice-wheat cropping system, (2) reduced-till CA-based rice-wheat-mungbean system, (3) no-till CA-based rice-wheat-mungbean system, and (4) no-till CA-based maize-wheat-mungbean system. The mean stratification ratio (SR) (i.e. a ratio of the concentrations of SOC and TN in the soil surface to those in a deeper layer) of SOC and TN for 0–5:5–10, 10–15, 15–20, 20–25 and 25–30 cm were found higher (> 2) under CA practices compared to intensive tillage-based conventional agricultural practice (< 2). No-till CA-based rice-wheat-mungbean system stored the highest amount of SOC (25.32 Mg ha⁻¹) whereas reduced till CA-based rice-wheat-mungbean system stored highest amount of TN (3.21 Mg ha⁻¹) at 0–30 cm soil depth. This study shows that CA stratifies SOC and TN and helps to enhance SOC sequestration and soil quality.