Understanding the nutritional and metabolic physiology of aquatic organisms is essential for optimizing aquaculture practices and informing ecological models. We investigated the influence of dietary composition, specifically the incorporation of multienzyme extract derived from Pleoticus muelleri waste, on the growth and metabolic processes of juvenile Cherax quadricarinatus. We investigated how these dietary changes influence dietary assimilation and tissue turnover using stable isotope δ13C and δ15N dynamics, in both the pleon muscle and hepatopancreas. Juvenile crayfish were subjected to two isocaloric diets for a 90‐day period: a control diet (diet C) and a diet supplemented with a multienzyme extract (diet E) from red shrimp waste. Despite comparable growth rates, isotopic analysis (δ13C and δ15N) of the pleon muscle and hepatopancreas revealed distinct metabolic patterns between both dietary treatments. The hepatopancreas exhibited accelerated isotopic turnover relative to muscle tissue, irrespective of diet, suggesting a more dynamic metabolic role. Diet E further accelerated turnover rates in both tissues, indicative of enhanced nutrient assimilation and utilization. Consistent isotopic disparities between the hepatopancreas and muscle tissues highlighted tissue‐specific metabolic functions, with the hepatopancreas serving as a metabolic hub. Molting‐induced shifts in isotopic patterns underscored the dynamic interplay between metabolic processes and nutrient mobilization. Isotopic equilibrium was reached earlier for δ13C than δ15N, with lower discrimination factors in the hepatopancreas. While δ13C primarily supported metabolic processes, δ15N contributed substantially to growth, especially in muscle. These findings illuminate the complex interplay of dietary composition, isotopic fractionation, and physiological regulation in C. quadricarinatus. The metabolic enhancements induced by the diet supplemented with the extract warrant further investigation to optimize nutrient utilization and growth performance in aquaculture settings.