ABSTRACT This study assesses the impact of different cropping systems on changes in total organic carbon (TOC), its fractions and biological activities to evaluate the changes in soil health. The rice-wheat cropping system (RWCS) had significantly higher total organic carbon (TOC) (38.8%) and soil organic carbon (SOC, 43.6%) compared to the pearl millet-mustard cropping system (PMCS). Active C pools were significantly higher in soils under cotton-wheat (CW) and pearl millet-wheat cropping systems (PWCS) than RWCS, whereas passive C pools (63% of TOC), the microbial biomass carbon (MBC) and dehydrogenase activity (DHA) were highest under RWCS than other systems. Soils under these cropping systems exhibited a significant polynomial relationship of TOC with SOC and dissolved organic carbon (DOC). Two significant canonical discriminant functions involving TOC, SOC, DOC, very labile carbon (CVL), labile carbon (CL), less labile carbon (CLL), recalcitrant carbon (CR), MBC and DHA could distinguish the different cropping systems and contributed 94.7%. The principal component analysis identified that TOC, SOC, pH and EC were the most reliable and contributing variables for assessing soil health under different cropping systems. Three PCs explained the 79.2% variability of the total variance of the original data set.