In a field study, long-term application of compost to a tropical Aeric Endoaquept under continuous rice growing in a rice–rice–fallow sequence resulted in the stimulation of microbial biomass and select soil enzyme activities. Mean seasonal soil microbial biomass-C (C mic) increased by 42%, 39% and 89% in inorganic fertilizer, compost and compost+inorganic fertilizer treatments, respectively, over the unamended control. C mic content was also influenced by the rice crop growth stage and was highest at maximum tillering stage irrespective of treatments and declined thereafter. Soil organic C (C org) content showed highly significant positive correlation with dehydrogenase, urease, cellulase, β-glucosidase and fluorescein di-acetate (FDA) hydrolysis activity, and a positive but not significant correlation with invertase and amidase activity. C/N ratio which was lowest in unamended control plots showed a significant positive relationship with only the enzymes involved in C cycle. Stepwise regression analysis revealed that for prediction of both total organic C and total N, FDA hydrolysis activity contributed significantly for the variance and explained up to 85–96% variability. Results demonstrated that microbial biomass and soil enzyme activity is sensitive in discriminating between long-term organic residue amendment practices.