This data set corresponds to the proteome of Streptococcus thermophilus 065 and corresponding extracellular vesicles (EVs) which were cultivated in M17 broth with lactose as carbon source. The bacteria were cultivated at 40°C for approximately 6 hours with and without Mitomycin C addition in the beginning of the exponential phase. For the proteome analysis, samples were collected at the end on the cultivation time in three biological replicates. EVs were collected by ultra-centrifugation. Bacterial cells were collected by centrifugation for 15 minutes at 6000×g, samples were frozen at -80°C until further use. Relative protein quantification was performed by Proteome Discoverer based on peptide intensity signals using default settings.