Intensive cropping with limited nutrient management options in low fertile semi-arid tropical soils will have agricultural sustainability problems in future. A better understanding of soil variables as influenced by long-term nutrient amendments could lead to the identification of more precise indicators to monitor soil fertility that would promote sustainability. Long-term nutrient experiment in semi-arid Alfisol at Coimbatore, India was investigated in two successive years, 2009 and 2010 to assess the enduring effects of organic (OM) and inorganic (IC) nutrient managements on soil variables. The organic amendments induced higher microbial population and enzyme activity compared to IC and control soils. The principal component analysis of observed variables revealed that soil organic carbon, microbial biomass carbon (MBC), dehydrogenase and alkaline phosphatase activity and diazotrophs population could be the possible indicators for predicting soil fertility resulting from long-term nutrient managements. The eubacterial community profile assessed by 16S rRNA gene sequence polymorphism revealed that the abundance and relative ratio of phyla belonging to Proteobacteria, Actinobacteria, Acidobacteria and Firmicutes were considerably affected due to either organic manures or inorganic fertilizers, and organic nutrient management favours bacterial community diversity. These results emphasize the importance of organic nutrient management to maintain soil biological properties in semi-arid Alfisol.