Animals may have target levels for lipid and protein stores which they try to maintain by feedback mechanisms. Thus, variation in initial body composition may be related to subsequent feed utilisation, for animals to maintain body composition in homeostasis. We assessed whether such relationships are genetically determined within a farmed population of European whitefish (Coregonus lavaretus) grown either on fishmeal or soyabean-meal diets. Soyabean meal is an increasingly-used ingredient in aquaculture feeds. Fish from thirty-five paternal families were analysed for initial body lipid and protein content, and for subsequent daily weight gain, daily feed intake, feed efficiency and their lipid and protein components. The results showed that none of the correlations of initial body lipid percentage with subsequent growth and feed utilisation were statistically significant. In contrast, low initial protein percentage was related to increased subsequent weight gain, protein gain and protein retention efficiency. This led to reversed ranking of families during growth for body protein percentage. Thus, mechanisms maintaining stable body lipid percentage across the population were weak, whereas the mechanisms stabilising body protein percentage were strong and successful. This explains the observations that cascades of lipid deposition occur during fish growth, leading to high amounts of phenotypic and genetic variation for percentage body lipid. In contrast, protein percentage remains phenotypically and genetically more invariable, reducing the potential for selective breeding. The soyabean-meal diet, in turn, induced only weak genotype x diet interactions, aiding in the genetic improvement of farmed fish to adapt to future feeds.