We previously demonstrated the existence of a naturally occurring metabolic disease phenotype in Libellula pulchella dragonflies that shows high similarity to vertebrate obesity and type II diabetes, and is caused by a protozoan gut parasite. To further mechanistic understanding of how this metabolic disease phenotype affects fitness of male L. pulchella in vivo, we examined infection effects on in situ muscle performance and molecular traits relevant to dragonfly flight performance in nature. Importantly, these traits were previously shown to be affected in obese vertebrates. Similarly to obesity effects in rat skeletal muscle, dragonfly gut infection caused a disruption of relationships between body mass, flight muscle power output and alternative pre-mRNA splicing of troponin T, which affects muscle calcium sensitivity and performance in insects and vertebrates. In addition, when simulated in situ to contract at cycle frequencies ranging from 20 to 45 Hz, flight muscles of infected individuals displayed a left shift in power-cycle frequency curves, indicating a significant reduction in their optimal cycle frequency. Interestingly, these power-cycle curves were similar to those produced by flight muscles of non-infected teneral (i.e. physiologically immature) adult L. pulchella males. Overall, our results indicate that the effects of metabolic disease on skeletal muscle physiology in natural insect systems are similar to those observed in vertebrates maintained in laboratory settings. More generally, they indicate that study of natural, host-parasite interactions can contribute important insight into how environmental factors other than diet and exercise may contribute to the development of metabolic disease phenotypes.