The impact of environmental perturbations (e.g., nitrogen (N), phosphorus (P), potassium (K) and rice straw (Rs)) on the dynamics of soil bacterial and archaeal community are multifactor dependent and seeks more investigation concerning underlying mechanisms. Current study was designed to establish the effect of pure and mixed fertilizers on microbial community profiles in paddy soil. A short-term microcosm based experiment was established in which each microcosm is amended with N as C(H2N)2O, P and K as KH2PO4, K as KCl and Rs with concentrations equivalent to 160 kg N ha−1, 60 kg P ha−1, 130 kg K ha−1 and 1% respectively. Soil pH, electrical conductivity (EC), total C (TC), total nitrogen (TN), organic matter (OM), available K (AK) and extractable P (EP) were evaluated. To understand the microbial community variation in soil and to predict their metabolic functions, a high throughput sequencing (HTS) approach of 16S rRNA gene along with phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) was employed and analyzed. The results showed that microbial richness and diversity were increased under all amendments compared to control. Proteobacteria, Actinobacteria and Firmicutes were dominant bacterial phyla. In all amendments, regarding relative abundance, Chloroflexi, Bacteroidetes and Verrucomicrobia showed positive while Actinobacteria, Acidobacteria and Gemmatimonadetes showed negative trends when compared with controlled observations. Thaumarchaeota and Euryarchaeota were dominant archaeal phyla and exhibited increasing and decreasing trends, respectively. The PICRUSt indicated microbial community shift significantly towards amino acid, carbohydrate, energy, and lipid metabolism while less towards glycan biosynthesis, synthesis of secondary metabolites, terpenoids and biodegradation. Regarding metabolism (methane metabolism), most and least responsive treatments were predicted to be KP and controls, respectively. These findings enhanced our understanding regarding soil quality, fertilizer composition and their impact on microbial diversity.