In order to support livelihoods, enhance food security, restore ecosystem services, and reduce pressure on forests, degraded land can be restored by utilising alternative land-use systems (ALUS), such as silviculture, silvipasture, and hortipasture techniques. ALUS significantly modify the dynamics of soil nutrients in both the surface and subsurface layers. Soils from the 0–15, 15–30, and 30–45 cm layers of Leucaena leucocephala (S)-, Hardwickia binata (H)-, Emblica officinalis (A)-, and Azadiracta indica (N)-based silviculture systems, Acacia nilotica-based silvipasture systems (SPS), natural grassland (NT), and fallow land (F) were sampled in order to better understand the nutrient dynamics of ALUS. Soils under S, H, and SPS had ~203%, 195%, and 129% higher organic carbon (SOC), respectively, than fallow land in the 0–15 cm soil layer. In the subsequent soil layer, those land-use systems had ~199%, 82%, and 110% higher SOC, respectively, than fallow land. Similarly, in the deeper layer, those land uses had ~232%, 23%, and 105% higher SOC, respectively, than fallow land. SPS and NT also improved the SOC concentration significantly over fallow land. Plots under S, H, and SPS had ~198%, 190%, and 125% higher available N, respectively, than fallow land in 0–15 cm soil layer. In the 15–30 cm soil layer, those land-use systems had ~19%9, 82%, and 110% higher available N, respectively, than fallow land. These systems also improved the P and K contents in subsurface soil. Micronutrient concentrations were also improved in soils under S, H, and SPS. Hence, ALUS’ adoption in degraded areas with trees provides a chance for C storage and improves the nutrient dynamics on degraded land.