Background/Objectives: Cationic surfactants are potential antimicrobial candidates. Even so, they are the foremost irritative and incompatible group, which limits their usage. The incorporation of surfactants in biopolymer-based nanoparticles is a feasible strategy to improve their efficacy and reduce those drawbacks. Methods: Surfactants with one amino acid on the polar head (lauroyl arginine methyl ester—LAM and phenylalanine dodecyl amide—PNHC12) and surfactants with two amino acids on the polar heads, arginine-phenylalanine (Lauroyl phenylalanine arginine methyl esther—C12PAM and phenylalanine-arginine dodecyl amide—PANHC12) were loaded to zein nanoparticles. Their antimicrobial and antibiofilm activities were evaluated. Also, the inhibitory activities of the surfactants and nanoparticles over skin-related enzymes were accessed in silico and in vitro, while their cytotoxicity was determined comparatively over immortal human keratinocytes (HaCaT) and human fibroblasts (3T3). Finally, the Vibrio fisheri luminescence reduction test was used to detect its ecotoxicity. Results: The nanoparticles were obtained successfully and exhibited good biocide activity against a wide range of pathogenic bacteria and yeasts. The surfactants were found active over the enzymes assayed: elastase > tyrosinase > collagenase > lipoxygenase, while the inhibitory activity was superior when nanoencapsulated over the enzymes tyrosinase and lipoxygenase. The surfactants and their corresponding nanoparticles presented acceptable cytotoxic levels, except for PNHC12 in both forms, while their ecotoxicity was limited and acceptable. Conclusions: Accordingly, the nanoencapsulation of the arginine-phenylalanine surfactants loaded to zein nanoparticles was found to be a smart strategy to enhance the antimicrobial activity and improve their selectivity over representative skin and connective tissues cell lines. These biological properties render the arginine-phenylalanine surfactant nanoparticles as promising candidates for antimicrobial and tissue repairing applications in wound treatments.