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Antibiotic resistance is a global problem, searching for new antimicrobial agents is an urgent need. In this study, in vitro antibacterial and antimicrobial effects of milk-derived antimicrobial agents, lactoferrin-derived peptides, lactoferricin (Lfc) and lactoferrampin (Lfa) (alone or in combination) and their association with natural extracts have been explored. The assessment of antimicrobial activity was based on two measurements: Minimum Inhibitory Concentration and Fractional Inhibitory Concentration indexes. Lfc alone is more suitable for inhibiting Staphylococcus intermedius and Malassezia pachydermatis, while Lfa against Candida albicans, a synergistic effect of the two peptides against all the three pathogens has been detected. A strong synergy of all the natural extracts with Lfc and Lfa solution against selected microorganisms in vitro was pointed out. Our results suggest that natural-derived compounds, such as milk peptides and vegetal extracts could be promising tools to treat moderate fungal and bacterial infections.