Dairy foods, especially of bovine origin, are the most common carriers of probiotics and conjugated linoleic acid (CLA)-producing microorganisms. The present study isolated probiotic strains from raw cow milk of the Lahaul valley capable of producing cis-9, trans-11 CLA isomer, besides exhibiting antioxidant properties with food formulation abilities. After preliminary probiotic screening, 34 strains were obtained, with 21 qualifying all the probiotic attributes and passing safety analysis. The seven most statistically promising probiotics were further explored for CLA production (16.87–28.01 μg/mL), and showed cis-9, trans-11 CLA isomer production as confirmed by GC-MS. To establish genomic evidence for safety analysis, whole genome sequencing was conducted for Enterococcus faecalis LJM:05, resulting in the deduction of antibiotic-resistance and virulence genes (lower identity scores). Based on the superior probiotic attributes, antioxidant, and CLA-producing properties, the strain Latilactobacillus curvatus LGM:16 was used to develop the curdled milk, with a legal, viable count (7.55 log10 CFU/mL) under pH ∼4.15 for 28 days of storage periods (4 °C). Scanning electron microscopic examination revealed microstructural changes after fermentation in the curdled milk compared to the control. The findings highlighted the role of indigenous probiotic strains with superior probiotic features, antioxidant activity, and CLA-producing ability in functional food formulation.