Microbial contamination is one of the main risks associated with drug production. The precise identification of the microbiota detected in the pharmaceutical production environment is essential for investigating sources of contamination, and for carrying out preventive and corrective actions. Studies using the Matrix-Assisted Laser Desorption Ionization-Time of Flight/Mass Spectrometry (MALDI-TOF/MS) methodology, which provides information about the bacterial proteome, have shown good rates in the identification of strains of pharmaceutical origin compared to other phenotypic methodologies, in addition to the high speed in obtaining results. The aim of this study was to compare two MALDI-TOF MS systems for the identification of bacterial strains isolated from an immunobiological manufacturing facility, not previously identified by the semi-automated system VITEK®2.