The impacts of variation in fish filleting by-products origin including white muscle (cod), dark muscle (herring) and farmed fish (salmon) on physicochemical and gel-forming properties of protein recovered using the pH-shift method were studied. The effects of different solubilization pHs (acid or alkaline) on protein yield/composition, and its properties were also studied. Alkaline version (pH 11.5–12.5) resulted in maximum protein yield for the three resources which ranked them as: salmon > herring > cod. Increasing solubilization pH from 11.5 to 12.5 increased protein yield in salmon and herring, while maximum protein yield of cod was obtained at pH 12. However, increasing solubilization pH from 11.5 to 12.5 required a two-fold higher amount of alkali compared to the adjustment to 11.5. All recovered proteins had gel-forming capacity; however, cod gels showed higher WHC and breaking force compared with salmon and herring protein gels. Increasing solubilization pH from 11.5 to 12.5 negatively affected the breaking force and color of the salmon and cod protein gels, but improved heme pigment removal, breaking force and whiteness of herring protein gels. The pH-shift process thus showed good potential for recovering high quality protein from the by-products, but protein solubilization pH should be carefully selected based on the target species.