The present study aimed to investigate the interaction effects of tomato seed mucilage (TSM) coating and shallot essential oil (SEO) (0%, 1%, and 2%) on the physicochemical, and microbial properties of Rainbow Trout (Oncorhynchus mykiss) during frozen storage (0, 1, 2, 3, and 4 months). The results indicated that the TSM coating treatments, especially, with the increase in SEO concentration effectively reduced the total viable count (TVC) and psychrotrophic bacteria count (PTC). Moreover, it decreasing the rate of changes in thiobarbituric acid (TBA), total volatile basic nitrogen (TVB-N), and peroxide value (PV). The TVB-N levels were within acceptable limits, except for the Ctrl treatment in the fourth month, where the TVB-N in fish fillet was exceeded 25 mg/100g. The incorporation of SEO to the TSM coating led to a decrease in pH variations, protein solubility, and moisture content of the Rainbow Trout fillets during frozen storage. At the end of the storage period, Hardness in the Ctrl treatment at the end of storage period were respectively 14.95%, 21.91%, and 24.52% lower than those in the TSM-0% SEO, TSM-1% SEO, and TSM-2% SEO treatments. Furthermore, at the end of the frozen storage period, the color changes in all treated fillets were significantly lower compared to the Ctrl treatment (p < 0.05). Overall, utilizing a 2% SEO-containing TSM treatment demonstrated the best performance in delaying undesirable qualitative changes. Hence, there is promising potential in using TSM as agricultural waste in combination with active compounds like SEO to produce an active coating. These coatings, according to their characteristics, can serve as a cost-effective, efficient, and safe option for preserving perishable marine products.