Information on the bioaccessibility of minerals is essential to consider a food ingredient as a potential mineral fortifier. In this study, the mineral bioaccessibility of protein hydrolysates from salmon (Salmo salar) and mackerel (Scomber scombrus) backbones and heads was evaluated. For this purpose, the hydrolysates were submitted to simulated gastrointestinal digestion (INFOGEST method), and the mineral content was analyzed before and after the digestive process. Ca, Mg, P, Fe, Zn, and Se were then determined using an inductively coupled plasma spectrometer mass detector (ICP-MS). The highest bioaccessibility of minerals was found in salmon and mackerel head hydrolysates for Fe (≥100%), followed by Se in salmon backbone hydrolysates (95%). The antioxidant capacity of all protein hydrolysate samples, which was measured by Trolox Equivalent Antioxidant Capacity (TEAC), increased (10–46%) after in vitro digestion. The heavy metals As, Hg, Cd, and Pb were determined (ICP-MS) in the raw hydrolysates to confirm the harmlessness of these products. Except for Cd in mackerel hydrolysates, all toxic elements were below the legislation levels for fish commodities. These results suggest the possibility of using protein hydrolysates from salmon and mackerel backbones and heads for food mineral fortification, as well as the need to verify their safety.