Latilactobacillus sakei has demonstrated significant potential as a probiotic in fermented foods; however, its role and impact as a co-fermenting agent in dairy products remain largely unexplored. This study investigated the effects of L. sakei CCFM1267 on the fermentation properties, physicochemical characteristics, and metabolite profiles of fermented milk. Two batches of fermented milk were prepared: one containing only Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus (BS), and the other containing L. bulgaricus, S. thermophilus and L. sakei (BSLs). Samples were collected during the 16-h fermentation period and at storage times of 2, 7 and 14 days for analyses of pH, water holding capacity (WHC), texture, viable bacterial counts, free amino acids (FAAs), volatile flavor compounds, and metabolomics analysis using untargeted approaches such as high-performance liquid chromatography-mass spectrometry (HPLC-MS). The addition of L. sakei CCFM1267 accelerated the fermentation process, resulting in consistently higher viable cell counts (maintaining levels above 106 CFU/mL) during fermentation and storage, improved WHC (p < 0.01), and enhanced viscosity (p < 0.05). Metabolomic analyses revealed significant increases in various FAAs (e.g., phenylalanine, leucine, valine, lysine, methionine, glutamic acid), ketone flavor compounds, and benzoic acid in the BSLs group. Notably, the BSLs fermented milk contained higher levels of acetylcholine and glycylproline, which are associated with antiinflammatory and immune response functions, respectively. These findings highlight the potential of L. sakei CCFM1267 as a valuable co-fermenting agent for developing fermented dairy products with enhanced nutritional value, sensory quality, and health-promoting properties.