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Sustainable agriculture plays a critical role in maintaining environmental health and also promotes long-term food security and the preservation of natural resources. We therefore, examined the response of intensified cropping systems over four years across five diverse cropland ecosystems viz. Basmati rice-Wheat-Cowpea, Basmati Rice-Potato-Wheat-Mixed Fodder (Maize + Cowpea + Charni), Basmati Rice-KnolKhol-Potato-Greengram, Basmati Rice-Radish-Green onion-French bean vegetable-Okra, and Rice-Fenugreek-KnolKhol-Green Onion-Dry Onion-Black gram to assess the changes in substrate availability and fertilizer application on nitrogen and phosphorus pools. Soil samples were collected from three different depths (0–5 cm, 5–15 cm, and 15–30 cm) during the kharif season. Significant results were observed in the mean values of mineralizable nitrogen, total nitrogen, ammonical nitrogen, nitrate nitrogen, and soil microbial biomass nitrogen at the 0–5 cm depth, with the highest values recorded under Rice-Fenugreek-KnolKhol-Green Onion-Dry Onion-Black gram. At the soil depth of 0–5 cm, available phosphorus and labile organic phosphorus exhibited significant differences, with the highest values observed in Basmati Rice-Potato-Wheat-Mixed Fodder. Moderately labile phosphorus reached its maximum values under T2 at both 0–5 cm, and at 5–15 cm depths. The peak values of non-labile organic phosphorus were found in T4 (Basmati Rice-Radish-Green onion-French bean vegetable-Okra) at the 0–5 cm soil depth. On a regional scale, the results suggest that more diversified cropping systems hold promise as sustainable agricultural practices that support nitrogen and phosphorus retention, contributing to overall soil sustainability.