Stable carbon and nitrogen isotope analyses were used to evaluate the contribution of five protein sources to the growth of juvenile slipper lobster Thenus australiensis. Protein sources tested were fish meal, krill meal, lupin meal, soybean meal and a squid by-product meal. A commercial in confidence basal mix was utilised to produce five experimental feeds containing 30% of each protein source. Juvenile lobsters were fed daily at 5% of their body weight for 12 weeks. Lobster performance was assessed by survival, feed intake and growth performance, and the effects of protein source on nutrient assimilation and discrimination factor were determined. The squid by-product meal, soybean meal, and krill meal produced better growth performance and survival. The specific growth rate on lupin meal was significantly (p < 0.05) lower than all the other protein sources. Apparent feed intake was significantly (p < 0.001) higher in squid by-product meal than lupin meal but with no significant differences in feed efficiency ratio. Protein source assimilation proportion in lobster ranged from 7% for soybean meal to 32% for squid by-product meal, whereby squid by-product meal and fish meal (29%) were the only protein sources assimilated at approximately their dietary inclusion level (30%). Overall, squid by-product meal had the best growth performance, high survival, and the highest assimilation into growth. This study demonstrated the potential of stable isotopic analysis to screen protein sources, evaluate the nutritional performance of the experimental feeds, and provide a deeper insight into ingredient utilisation. This study also provides the first whole-body isotopic discrimination factors for juvenile lobster, which can determine ingredient contribution to growth in future studies.