A detailed study was conducted to investigate the long-term effects of rice–wheat and poplar-based agro-forestry systems existing on a large area for last 25 years on the distribution of macro as well as micronutrients in surface soils, as well as their profiles. To achieve these objectives, profile soil samples (0–150 cm) were collected from 10 randomly scattered locations each from rice–wheat and poplar-based agro-forestry systems and analyzed for various physico-chemical properties. The results of our investigation revealed that pH, EC, OC available N, P and K reported significantly higher levels in agro-forestry as compared to rice–wheat system. On the other hand, DTPA-extractable and total Zn, Cu, Fe and Mn were significantly higher in D1 (0–15 cm), D2 (15–30 cm) and D3 (30–45 cm) depths of rice–wheat system which may be attributed to the reduced conditions prevailing during rice crop. Nutrient budgeting also assessed the impact of crop removal and fertilizer inputs along with recycling of crop residue and leaf litter. Also, the build-up of available nutrient status in surface layer (0–15 cm) and soil profiles (0–150 cm) continuously under these two systems helped in maintaining agricultural sustainability and soil fertility over a long period of time.