Chitosan (CS) nanoparticles were formed by two different methodologies: ionic (with sodium tripolyphosphate ‐TPP) and chemical (with genipin ‐GN) cross‐linking. CS–TPP and CS–GN nanoparticles showed positive zeta potential (+46.24 and +62.86 mV, respectively) and sizes ranging from 83.70 to 835.91 nm, respectively. Ionic cross‐linking (with TPP) resulted in particles smaller than those formed by chemical cross‐linking (with GN). The in vitro antibacterial activity revealed an efficient inhibitory effect, especially regarding CS–TPP. In situ, antibacterial and antioxidant studies were carried out on O/W emulsions. The mesophilic and psychrotrophic counts, peroxide value and quantification of conjugated dienes and trienes during time revealed that nanoparticles tend to improve the microbiological and oxidative stability of emulsions. These findings underline the direct relationship between the reduction of particle size and the increase in biopolymer functional properties and expand the possibilities of CS application as a natural preservative of emulsified systems.