To ensure year-round availability and stability of Atlantic mackerel caught in Icelandic waters during summer after intensive feeding, freezing is essential. Due to the high lipid content and sensitive lipid composition of the fish caught at this time, the fish industry requires detailed research to understand the mechanisms underlying the degradation processes occurring during storage and processing, in order to develop high-value hot-smoked products. Therefore, the impact of frozen storage at -25 ± 1.8 °C (for 6, 9, and 20 months) prior to hot-smoking, was investigated on the physicochemical, microbial, and sensory quality of deep-skinned, smoked fillets from well-fed Atlantic mackerel caught in late August. The stability of hot-smoked fillets stored at 1 ± 0.6 °C was then monitored for 28 days. Total aerobic viable counts (TVC) remained below acceptable thresholds due to the combined effects of brining, freezing, and hot-smoking, while Listeria monocytogenes was not detected in the hot-smoked products. Slow formation of oxidation products was observed during the chilled storage, especially in the fish frozen for 9 months. Minor lipid deterioration was also detected during sensory analysis, but all spoilage indices remained within acceptable thresholds for shelf-life. Frozen storage for up to 20 months thus effectively maintained the sensory acceptability and suitability of deep-skinned mackerel fillets, making them an excellent choice for the fish-smoking industry.