Chhurpe is a naturally fermented traditional dairy food of high altitude Western Himalayan region. They are generally prepared from cow or yak milk and are consumed during harsh winters. The present study was conducted to characterize the different Chhurpe samples traditionally prepared by the ethnic groups utilizing milk from different animal breeds such as cow, yak, Zomo (cow × yak), and Germo (Zomo × yak). Nutritional characterization revealed that 100 g of Chhurpe could completely meet the dietary protein requirements of children and adults with high concentrations of methionine and lysine. Tryptophan and valine were the limiting amino acids among all the Chhurpe samples. Palmitic, stearic, and oleic acids were the predominant fatty acids. The Chhurpe samples were a rich source of micronutrients such as calcium, iron, and zinc meeting above 70% of recommended dietary allowances (RDA) among children (3–10 years) and up to 20% RDA for adults. Culture-independent metagenomic analysis revealed that lactic acid bacteria were the predominant group, consisting of genera such as Lactobacillus, Leuconostoc, Lactococcus, and Streptococcus followed by acetic acid bacteria, mainly Acetobacter. At the species level, Lactobacillus delbrueckii was the abundant strain among all the Chhurpe samples. Species diversity was significantly higher in Chhurpe prepared from Zomo milk. Probiotic bacterial strains such as Lactobacillus helveticus, L. delbrueckii, L. brevis, and Leuconostoc mesenteroides were identified in the Zomo Chhurpe indicating their superior quality. The present study was an attempt to popularize Chhurpe and promote its wider consumption by highlighting its nutritional properties.