Purpose Vitamins and SCFA (short-chain fatty acids) production from Lactobacillus isolates are studied due to its health benefits to the human hosts. Lactobacillus strains are widely used in fermented foods, and few of them are reported with vitamin and SCFA production potential. Therefore, in the present study, vitamins and SCFA production capability of isolates were studied to find the potent Lactobacillus cultures for value-added functional food product development. Methods Five Lactobacillus strains, i.e., KGL2, KGL3A, KGL4, RNS4, and WTS4, were isolated from rice-based traditional fermented foods of Garo Hills, Meghalaya, India. All the well grown isolates were morphologically, physiologically, and genetically characterized. Then, vitamins and SCFA were estimated using HPLC based methods. Vitamins produced in vitamins free assay medium and SCFA in milk medium are produced by Lactobacillus. Results Lactic acid bacteria produce essential vitamins like riboflavin, folate, cobalamin, and SCFA which have health impacts (anti-obesity, anti-diabetics, anti-microbial, and other chronic diseases prevention) to the host. These vitamins are essential for cellular and metabolic growth of living system. In the study, five potent Lactobacillus isolates viz., KGL2 (Lactobacillus fermentum), KGL3A (Lactobacillus plantarum), KGL4 (Lactobacillus fermentum), RNS4 (Lactobacillus rhamnosus), and WTS4 (Lactobacillus fermentum) were considered for vitamins (B 2 , B 12 , and B 9 ) and SCFA productions (lactate, butyrate, and acetate). However, KGL3A had shown highest B 2 production (0.7 μg/ml) while KGL2 exhibited maximum B 12 production (0.05 μg/ml) after 36 h. Moreover, WTS4 attributed highest folate production (0.09 μg/ml) after 24 h. In addition, RNS4 reported the maximum short-chain fatty acid production (0.77 g/l acetic acid, 0.26 g/l lactic acid, and 0.008 g/l butyric acid respectively). Conclusions Potent Lactobacillus isolates from traditional fermented foods of Garo Hills, Meghalaya, India (North East Part of India) showed maximum production of B 2 , B 9 , and B 12 as well as short-chain fatty acids and could be used for their application as health beneficial functional fermented dairy products.