The current study aims to co‐encapsulate Shirazi thyme (Zataria multiflora) essential oil (ZEO) and nisin into chitosan nanogel as an antimicrobial and antioxidant agent to enhance the shelf‐life of cheese. Chitosan‐caffeic acid (CS‐CA) nanogel was produced to co‐encapsulate Zataria multiflora essential oil and nisin. This nanogel was characterized by dynamic light scattering (DLS), Fourier Transform Infrared (FTIR) spectroscopic analysis, X‐ray diffraction (XRD) analysis, and scanning electron microscopy (SEM) images. The effect of free (T_FZN) and encapsulated ZEO‐nisin in chitosan nanogel (T_CZN) on the chemical and microbiological properties of Iranian white cheese was assessed. The particle size, polydispersity index value (PDI), zeta potential, antioxidant activity, and encapsulation efficiency of the optimal chitosan‐ZEO‐nisin nanogel were 421.6 nm, 0.343, 34.0 mV, 71.06%–82.69%, and 41.3 ± 0.5%, 0.79 ± 0.06 mg/mL. respectively. FTIR and XRD approved ZEO and nisin entrapment within chitosan nanogel. The chitosan nanogel showed a highly porous surface with an irregular shape. The bioactive compounds of ZEO and nisin decreased the pH changes in cheese. On the 60th day of storage, the acidity of treated samples was significantly lower than that of control. Although the lowest anisidine index value was observed in samples treated with sodium nitrate (NaNO₃) (T_S), there was no significant difference between this sample and T_CZN. The lowest microbial population was observed in T_CZN and T_S. After 60 days of ripening, Coliforms were not detected in the culture medium of T_CZN and T_S. The results can contribute to the development of a natural preservative with the potential for application in the dairy industry.