The rapid expansion of the aquaculture industry with carnivorous fish such as salmon has been accompanied by an equally rapid development in alternative feed ingredients. This has outpaced the ability of prevailing authentication method to trace the diet and origins of salmon products at the retail end. To close this gap, we developed a new profiling tool based on amino acid delta C-13 fingerprints. With this tool, we discriminated with high-accuracy among wild-caught, organically, and conventionally farmed salmon groups, as well as salmon fed alternative diets such as insects and macroalgae. Substitution of fishmeal with macroalgae was detected at 5% difference level. The delta C-13 fingerprints of essential amino acids appear particularly well suited for tracing protein sources, and the non-essentials for tracing lipid origins (terrestrial vs. aquatic). In an industry constantly developing new feed proteins and functional additives, our method is a promising tool for tracing salmon and other seafood products.