The people of the Indian North-western Himalayas consume various traditional fermented foods, which may contribute to their healthy lifestyle. However, the probiotic diversity of the region is largely unknown. In the current study, indigenous Himalayan traditional foods (dairy products and alcoholic beverages) were investigated for probiotic diversity via culture-based and culture-independent methods and metabolites study. The culture-based taxonomic classification revealed the prevalence of probiotic genera Levilactobacillus, Latilactobacillus, Limosilactobacillus, Lactiplantibacillus, Lacticaseibacillus, and Companilacobacillus, which differed from the genera identified through amplicon sequencing. Alpha diversity analysis revealed higher probiotic diversity in fermented dairy products (FDPs) than in the alcoholic beverages samples. Redundancy analysis revealed that food’s properties, like fat, ash, & moisture content, temperature, and electrical conductivity, influence the probiotic diversity in the samples. Additionally, Gas chromatography-mass spectrometry (GC-MS) analysis identified high levels of methyl hexadecanoate and methyl linoleate in the food products. Metabolic functional predictions showed the dominance of anabolic pathways in dairy samples and catabolic pathways in alcoholic beverage samples. Overall, FDPs with superior nutritional properties and probiotic diversity could be considered a better choice as functional food.