In the last two decades, the productivity of Rice-wheat cropping system in the upper Indo-Gangetic Plains of India has stagnated and now in a declining trend. As a result, farmers shifted to a different cropland grown systems so as to achieve a higher net productivity. This study aim to assess as how nutrient index (NI), microbial diversity and soil quality changed after replacement of rice-wheat by vegetable (VGS), pulse (PGS), potato (PoGS) and mustard (MGS) grown system. An analysis of 307 soil samples from various croplands revealed a soil pH range of 6.58-8.87 with 75.3% soils under low category of mineralized N (MN) resulting in its low NI (<1.67). The highest NI, enzymatic activity and microbial biodiversity was recorded under PGS, which restored 34.2, 24.1 and 10.2% greater SOC, carbon substrate oxidation rate and MN than PoGS, respectively. The diversity indices were the highest in PGS followed by VGS, but soil quality index was 0.783 (VGS), 0.771(PGS), 0.695 (WGS), 0.663 MGS), and 0.647 (PoGS). The silt content, SOC, Zn, total N, acid phosphatase activity (ACP), available P and total culturable fungi were the key soil indicators across the cropland grown systems. Among the cropland systems, silt content, SOC, total N and ACP were the main soil indicators for PGS, whereas, silt content, SOC, P and Zn were the ideal indicators for VGS that affected microbial dynamics and soil quality. Overall, it is concluded that PGS maintained higher nutrient index, microbial and functional diversity, but VGS improve greater soil quality.