Impacts of processing technology (mechanical separation and pH-shift processing) on protein recovery from salmon, herring and cod backbones and the content of macro- and micronutrients in the recovered protein enriched products were investigated. Mechanical separation led to higher protein recovery compared with the pH-shift process and using both techniques, recovery ranked the species as herring > salmon > cod. However, the pH-shift process up-concentrated protein from herring and salmon backbones more efficiently than mechanical separation by removing more fat and ash. This consequently reduced n-3 PUFA and vitamin D content in their protein isolates compared with the backbones and mechanically separated meat (MSM). Cod protein isolate, however, contained higher levels of these nutrients compared with MSM. Mechanical separation concentrated vitamins E and C in salmon MSM but not for cod and herring. Opposite, pH-shift processing reduced levels of these two vitamins for cod and herring backbones, while vitamins D and C were reduced for salmon. For minerals, selenium, calcium, magnesium, and potassium were lower in protein isolates than MSM, while copper, zinc, iron and manganese were similar or higher. Overall, there is a major potential for upcycling of fish backbones to food ingredients, but processing technology should be carefully balanced against the desired nutrient profile and final application area.