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A study was conducted to investigate the effect of chemical fertilizer, organic manure and two cropping systems viz., pearlmillet - clusterbean - castor rotation and upland rice - lentil sequence on microbial quotient (MQ), metabolic quotient, specific enzyme activity (dehydrogenase, arylsulfatase and urease) and microbial biomass carbon (MBC) in long-term (1821 years) field experiments in Entisols of semi-arid region of Gujarat and Inceptisols of sub-humid region of Varanasi. Higher MQ values were recorded in Entisols than Inceptisols. MQ ranged from 4.00-5.08 and 1.00-1.85 % across soil layers in Entisols and Inceptisols, respectively. Metabolic quotient values ranged from 0.11-0.23 and 0.04-0.07 across soil layers in Entisols and Inceptisols respectively. The specific enzyme activity of dehydrogenase was maximum in Entisols, whereas, arylsulfatase and urease activity was recorded more in Inceptisols. Higher specific enzyme activity reflects greater microbial activity and microbial biomass turnover. Agro-ecosystem in sub-humid region resulted in 1.5 fold higher geometric mean of enzymes (GMea) than in semi-arid region. The application of 50% RDNF (recommended dose of N-fertilizer) + 50% RDN FYM (farm yard manure) in Entisols and 50% N (FYM) + 50% RDF in Inceptisols improved microbiological activities (GMea) at both the sites. The concentration of soil organic carbon (SOC) and MBC were significantly correlated with GMea in both agro-ecosystems. In conclusion, integrated sources of nutrients with inclusion of FYM and 50 % reduction of fertilizers improved the microbiological activities in both Inceptisols and Entisols.