The mandacaru is a cactus species complex widely known in Brazil, with extensive applications in medicinal, food, and agricultural fields. Although it is used medicinally by traditional populations, to treat several diseases, knowledge about its biomolecules of biotechnological potential is still limited, specifically regarding antimicrobial and healing properties. The bacterial resistance to conventional antibiotics presents a significant challenge in modern medicine. In light of this scenario, bioprospecting mandacaru for biotechnological applications as an antimicrobial has emerged as a new and promising research area. In this study, transcriptomic data from three Cereus species (C. fernambucensis, C. hildmannianus, and C. jamacaru) were combined with bioinformatic approaches, including protein modeling, molecular docking, and molecular dynamics simulations, to identify proteins with therapeutic potential for treating wound infections. Our findings highlighted peptides as particularly promising antimicrobial agents, demonstrating efficacy against a range of pathogens, including Gram-positive and Gram-negative bacteria, as well as fungi. Those peptides showed strong interactions with the streptolydigin and sodium ligands, with the streptolydigin ligand emerging as the most promising for enhancing antimicrobial activity. Molecular dynamics revealed that while CF15 exhibited limited stability, CF267, CF48, CH167, and CH176 displayed superior stability, positioning them as the most promising candidates for further investigation. Future work will focus on synthesizing these peptides and evaluating their antimicrobial properties through in vitro and in vivo analyses, to develop them into potent therapeutic agents.