Infections with bacterial pathogens are a major cause of morbidity and mortality worldwide. Furthermore, the extensive use of antibiotics increased the frequency of infections with drug-resistant pathogens. Streptococcus pneumoniae, a major cause of bacterial pneumonia, is among the pathogens that often show resistances. As an additional side effect, the use of antibiotics can disrupt the patient’s intestinal microbiome, allowing Clostridioides difficile to cause severe, recurring and hard-to-treat colitis. Hence, new antimicrobials are needed to combat infections caused by these pathogens. A promising approach is the usage of antimicrobial peptides (AMPs), defense molecules produced by organisms from all domains of life. AMPs can specifically perforate bacterial membranes and stimulate the overall immune response of the host. In this work, the proteomic adaptations of S. pneumoniae to the human antimicrobial peptides LL-37 and hBD3 were assessed by high-resolution mass spectrometry and compared to general membrane stress, in order to evaluate the specificity of the bacterial reactions. Furthermore, C. difficile was challenged with the Lactococcus lactis-derived AMP nisin, and the proteomic alterations were examined. In essence, application of LL-37 and hBD3 changed the abundance of pneumococcal proteins involved in membrane transport, including a putative AMP transporter, a protease, virulence proteins and genetic regulators. Moreover, a challenge with LL-37 caused an ...