Second cheese whey (SCW), the nutrient-rich by-product of whey cheese production, presents both an environmental challenge and an opportunity for sustainable innovation in the dairy sector. While Italy generates up to one million tons of SCW annually, its potential remains largely untapped, particularly by small and medium-sized dairies that often use it for animal feed or discard it as waste. This study investigates how variability in SCW composition influences its fermentation by different strains of Propionibacterium freudenreichii and whether this process consistently enhances the nutritional profile of SCW. To this end, five strains selected based on physiological and functional traits were tested on different SCW samples. Untargeted metabolomics revealed that SCW composition shaped fermentation outcomes while highlighting strain-specific impacts on the metabolome. Across all fermented samples, 45 metabolites were consistently enriched, including derivatives of vitamins B9 (folate) and B12 (cobalamin), essential amino acids, and compounds with prebiotic and antioxidant functions. Pathway analysis indicated significant activation of the “one-carbon pool by folate” pathway and glycine, serine, threonine, and vitamin B6 metabolism. These results demonstrate the ability of P. freudenreichii to transform SCW into a nutritionally enriched product, offering a promising, zero-waste strategy for valorizing dairy by-products within a circular economy framework.