Every year, millions of foodborne illnesses with thousands of deaths occur worldwide, which is why controlling foodborne pathogens is sought. In this study, nanoemulsions of phytochemicals extracted from Plectranthus hadiensis var. tomentosus (PHT) were obtained, and their antioxidant and antimicrobial capacities were evaluated. PHT extracts were obtained by maceration, ultrasound, and Naviglio methods, and their antimicrobial activity against Staphylococcus aureus, Listeria monocytogenes, Escherichia coli, and Salmonella enterica was determined by the microdilution method. The extract with the highest antimicrobial activity was obtained by Naviglio with a minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of 12.5 and 25 mg/mL, respectively, for all bacterial strains. The nanoemulsion (o/w) made with Tween 40, 5% extract, and 50% ultrasonic amplitude had a globule size of 4.4 nm, a polydispersity index of 0.48, and a surface charge of −0.08 mV and remained stable for 30 days. This nanosystem presented significantly higher antimicrobial and antioxidant activity than the free extract. Thus, the nanoencapsulation of the phytochemicals in the PHT extracts is an alternative to protect and enhance their biological activity against pathogenic microorganisms.