Nano-encapsulation of essential oils, a specific area of interest, can help overcome challenges associated with their commercial use. This study aimed to evaluate the effect of different concentrations of chitosan, Ziziphora clinopodioides L. essential oil (ZcEO), and Sodium-Tri Polyphosphate (TPP), both individually and in interaction, on several properties of EO-loaded chitosan nanoparticles. These properties include particle size (PS), zeta potential (ZP), and encapsulation efficiency (EE) using a two-stage emulsion-ionic gelation approach. The optimization of the parameters was done by response surface methodology using Box-Behnken design. The chemical composition of ZcEO was analyzed as well. The primary compounds in ZcEO were found to be pulegone (29.24 %), 1,3-dimethyl-2-(2-methylpropylidene) imidazolidine (9.05 %), piperitenone (6.65 %), thymol (5.38 %), and carvacrol (5.27 %). The PS ranged from 117.33 to 4934.1 nm, the ZP varied from -1.1 to -30.83 mV, and the EE spanned from 31.74 to 87.04 %. The results showed that an increase in the initial EO content led to a decrease in PS and ZP, but an increase in EE. Moreover, increasing the TPP concentration resulted in an enhancement in PS, ZP, and EE, whereas increasing the Chs concentration led to a slight increase in PS, ZP, and EE. Furthermore, the results of this study proved the interaction effect of different parameters on the responses investigated. Under optimized conditions, the optimal concentrations of chitosan, ZcEO and TPP were attained at 6.768, 6.078, and 7.595 mg/mL respectively. This resulted in a PS of 117.331 nm, a ZP of -20.949 mV, and an EE of 75.385 %. In conclusion, the results suggest that adjusting the concentrations of Chs, EO, and TPP is an effective approach to controlling the properties of NPs and optimizing their performance.