Abstract The aim of this study was to evaluate the performance of Caspian Sea-style spontaneous milk fermentation to improve the quality of pasteurized milk containing high levels of Pseudomonas contamination, with a focus on microbiological safety and stability of the final product. Bacterial diversity of pasteurized milk, fermentation process, and after 60 days of storage was analyzed by Illumina-based sequencing, and presence of viable taxa was confirmed by culturing on selective media. Low quality pasteurized milk harbored mainly Gram-negative bacteria, markedly dominated by Pseudomonas. Following fermentation, lactic acid bacteria rapidly became dominant with maximum population of 10.15 log CFU/mL at 18 h, represented mainly by Lactococcus. However, sequences related to Pseudomonas, and to a lesser extent for enterobacteria, remained constant throughout the fermentation process. The cultured-dependent approach confirmed the presence of viable Pseudomonas, with a final population of 5.60 log CFU/mL. Biochemical transformations were further analyzed, indicating lactic acid as the main end-metabolite produced (maximum concentration of 5.93 g/L at 24 h). In addition, the increase of 2-nonanone can be correlated as a volatile biomarker of P. aeruginosa and related species. Altogether, the results demonstrated that natural milk fermentation may often not inhibit the development of pathogens and food spoilage microorganisms.