The aim of this work was to obtain chitosan nanoparticles (<1000 nm) with chincho (Tagetes elliptica Sp.) essential oil (CEO-CSNPs) using the ionic gelation method. A Box–Behnken design (BBD) was applied, using chitosan solution (CS) pH (4.0, 4.4, 4.8); the mass ratio of CS/CEO (1:0.7, 1:0.85, 1:1.0) and the mass ratio of CS/CS-tripolyphosphate (1:0.46, 1:0.58, 1:0.7) as independent variables. The formulation-dependent variables, encapsulation efficiency (EE) and loading capacity (LC) of the CEO-CSNPs were evaluated. BBD determined that optimal conditions for CEO-CSNPs were pH: 4.4, CS/CEO mass ratio 1:0.7 and CS/TPP mass ratio 1:0.46. Once the optimization was defined, particle size (PS), zeta potential (ZP), polydispersity index (PDI), CEO-CSNPs morphological studies, in vitro CEO release, and antibacterial activity were determined. The CEO-CSNPs showed an EE of 52.64% and a LC of 11.56%, with a diameter of 458.5 nm, with a ZP of 23.30mV, and a PDI of 0.418. The SEM studies showed that the nanoparticles were rounded and had uniform shapes. In addition, CEO-CSNPs showed a minimum inhibitory concentration against Staphylococcus aureus, Salmonella infantis and Escherichia coli of 5.29, 10.57 and 10.57 µg/mL, respectively. These results could be very useful for the stabilization of chincho essential oil for food industry purposes. However, several studies about the release, as well as interaction with food matrices, will be necessary.