The climate change effects are eliciting a worldwide search for solutions to reduce carbon (C) and nitrogen (N) emissions from agricultural soils, especially in semi-arid areas. Therefore, it is crucial to explore new dimensions and perspectives for enhancing subsurface soil C sequestration, particularly in agricultural soils of semi-arid areas, where most of the C and N is lost because of oxidation. Our approach involves adjusting the crops and cropping systems to improve subsoil C and N sequestration. We therefore studied the impact of long-term agricultural land use types (LUT's) viz., Soybean + Pigeon pea (LUT-1), Soybean - Chickpea (LUT-2), Cotton + Pigeon pea (LUT-3), Soybean - Wheat (LUT-4), Sugarcane (LUT-5), Cotton (LUT-6) and Fallow (LUT-7) on dynamics of C and N at surface and subsurface soil layers (0-20, 20-40, 40-60 and 60-80 cm depth). The results showed that LUT-4 showed significantly highest values of soil organic carbon (SOC), water soluble carbon (WSC) and permanganate oxidizable carbon (KMnO4-C) at all soil depth. Similarly, LUT-4 showed the improvement in SOC and TOC-stock up to 20.1 and 42.7 Mg ha(-1) at surface (0-20 cm), 25.9 and 67.3 Mg ha(-1) at sub-surface (20-60 cm) and 45.8 and 109.8 Mg ha(-1) in profile (0-80 cm) over Fallow. The distinctive improvement of stratification ratio's (SR's) of SOC and TOC showed the improvement in soil quality under different LUT's. The LUT's with soybean and pigeon pea as crop component showed highest improvement in soil microbial biomass carbon (MBC), microbial respiration (MR) and metabolic quotient (qCO(2)) as compared with other LUT's following the sequence: LUT-4 > LUT-3 > LUT-1 > LUT-2. Although LUT-5 showed higher values of N fractions permanganate oxidizable-N (KMnO4-N), nitrate-N (NO3-N) and ammoniacal-N (NH4-N), LUT's like 1, 2, 3 and 4 also recorded significant improvement. The significantly higher total nitrogen (TN) stock was recorded under LUT-4 followed by LUT-3, LUT-1 and LUT-2. Depth wise estimation of carbon pool management index (CPMI) and nitrogen pool management index (NPMI) indicates that LUT's 1-4 were better options for enhancing deep soil C and N sequestration and implementing carbon neutral policies in semi-arid ecosystems.