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Antimicrobial peptides (AMPs) possess bactericidal activity against a variety of pathogens depending on an overall balance of positively charged and hydrophobic residues. Selective fluorination of peptides serves to fine‐tune the intrinsic hydrophobicity and that could improve AMP bioactivity without affecting the sequence length. Only a few studies have focused on the impact of this unique element on antimicrobial potency and came to somewhat contractionary results. Moreover, the influence of fluorinated amino acids on peptide proteolysis is yet not fully understood. In this work, we tackle the link between side chain fluorination and both antimicrobial activity and proteolytic stability for two series of amphiphilic β‐hairpin peptides. In particular, a synergy between antimicrobial activity and peptide hydrophobicity was determined. All peptides were found to be barely hemolytic and non‐toxic. Most surprisingly, the fluorinated peptides were susceptible to enzymatic degradation. Hence, the distinctive properties of these polyfluorinated AMPs will serve for the future design of peptide‐based drugs.