The chemical composition of the insect cuticle varies remarkably between species and their life stages. It can affect host resistance and substrate utilization by invading entomopathogen fungi, such as the soil fungus Conidiobolus coronatus. In this study, Sarcophaga argyrostoma flies were exposed to sporulating C. coronatus colonies for 24 h; the pupae were resistant, but the adults demonstrated 60% mortality. Although the pupae demonstrated no sign of infection nor any abnormal development, our findings indicate that after 24 h of contact with the fungus, the pupae demonstrated a 25.2-fold increase in total cuticular free fatty acids (FFAs) and a 1.9-fold decrease in total internal FFAs. Also, the cuticular FFA increased from 26 to 30, while the internal FFA class increased from 13 to 23. In exposed adults, the total mass of cuticular FFAs increased 1.7-fold, while the number of FFAs stayed the same (32 FFAs). Also, the internal FFA class increased from 26 to 35 and the total FFA mass increased 1.1-fold. These considerable differences between adults and pupae associated with C. coronatus exposure indicate developmental changes in the mechanisms governing lipid metabolism and spatial distribution in the organism, and suggest that cuticular lipids play a vital role in the defence against pathogenic fungi.