The effects of the encapsulation of Satureja bachtiarica essential oil with chitosan on the shelf life and quality of pomegranate seeds were studied in an experiment based on a completely randomized design with eight treatments, including different ratios of chitosan to S. bachtiarica essential oil (control, 1:1–0.3, 1:1–0.6, 1:2–0.3, 1:2–0.6, 1:3–0.3, 1:3–0.6) and three replications. The results showed that the highest fruit extract pH was observed in the control treatment before the storage period. The post-storage control treatment exhibited the highest total soluble solids (TSS). The highest organic acid was obtained from the extract treated with the chitosan: essential oil ratio of 0.6-1 and from the control plants before the storage period. The post-storage control treatment had the lowest organic acid content. During the storage period, anthocyanin content was decreased significantly relative to the control treatment before the storage period. The chitosan:essential oil ratios of 3-0.3 and 3-0.6 brought about the highest antioxidant capacity. During the storage period, the application of chitosan:essential oil ratio of 2-0.6 increased phenol content compared to the control before the storage period. The highest weight loss was observed in the treatment of chitosan:essential oil ratio of 3-0.6. Overall, coating pomegranate seeds and selecting an appropriate concentration of S. bachtiarica for incorporation into the chitosan coating can contribute to preserving the shelf life, marketability, and nutritional quality of pomegranate seeds.