The study aimed to verify the relationship found between individual indicator traits, derived from an isotope ratio of 13C/12C in various tissues (muscle, liver, and adipose), and individual feed efficiency. A 50-day experiment was performed with 46 rainbow trout (Oncorhynchus mykiss) kept in individual tanks after a dietary switch, using an experimental feed based on maize gluten with an enhanced level of 13C, during the grow-out phase. Individual growth, feed intake, and isotope profiles (muscle, liver, fin, and adipose tissue) were recorded. Using a Lasso-regression model, feed efficiency was found to be positively associated with visceral adipose tissue synthesis, meaning that feed efficiency was worsened when visceral adipose synthesis increased. The results indicated that deposition efficiency through lipid metabolism (δ13C in adipose tissue) was the most important determinant of feed efficiency of rainbow trout at this life stage. The results suggest that phenotyping of lipid deposition efficiency is possible through the use of feed ingredients with a natural abundance of stable isotopes.