Rice beer is traditionally prepared and consumed by various ethnic populations in the Southeast Asian countries. To understand the probable effects of rice beer on human health, present research was aimed to study biochemical parameters, microbial diversity and metabolites of major rice beer varieties of Assam, namely Apong (Poro and Nogin), Xaaj and Joubishi. Alcoholic content of rice beer varieties varied from 9.41 to 19.33% (v/v). Free radical scavenging activity against DPPH• and ABTS + were 1.94-4.14 and 1.69-3.91 mg of ascorbic acid/ml of rice beer, respectively. In relation to antioxidant activities, phenolic content varied from 2.07 to 5.40 mg gallic acid/ml of rice beer. Next-generation sequencing of 16S rDNA showed that 18 genera of bacteria were present irrespective of rice beer varieties in which lactic acid bacteria were the dominant group (90% abundance). Functional predictions based on the bacterial profiles indicated pathways, such as metabolisms of carbohydrate, amino acid, vitamins and cofactors, and xenobiotic biodegradation, to be active in the rice beer varieties. Out of 18 core bacterial genera, 7 had correlations with the predicted functions. Gas chromatography and mass spectroscopy-based metabolite analysis revealed that the metabolite profiles of the rice beer varieties consisted of 18 saccharides, 18 organic acids, 11 sugar alcohols, 8 amino acids, 1 vitamin and nutraceutical compounds thiocoumarine, carotene, oxazolidine-2-one and acetyl tyrosine. Due to the presence of potent prebiotics, probiotics and nutraceuticals, rice beer may have health benefits which need to be studied further.