Growing fish consumption worldwide has driven fish processors to introduce innovative seafood products with extended shelf-life and desirable organoleptic properties. This study investigates the impact of freezing deep-skinned Atlantic mackerel fillets before and after smoking, prior to canning. Physicochemical and organoleptic properties of canned fillets were evaluated after 1 and 12 months of storage at room temperature. The formation of primary oxidation products (PV) was similar in both cases, while the secondary oxidation products (TBARS) were significantly lower when the fillets were smoked before freezing. PV and TBARS were significantly lower in all canned mackerel samples after prolonged canned storage compared to the shorter storage. However, lipid oxidation and hydrolysis were very limited after both treatments and, therefore, do not constitute an issue in these products. Results of product evaluation and instrumental texture analysis of canned mackerel indicated more beneficial characteristics (firmer fillets, nor mushy) when fillets were frozen first and then hot-smoked (FSC). Fillets that were smoked first and then frozen (SFC), regardless of the canning storage time, were characterized by a mushy texture and appearance, which can negatively impact consumer acceptance. Therefore, freezing prior to hot-smoking may represent a better choice if the fillets are intended for canning.