Parasites can affect host behavior, cognition, locomotion, body condition and many other physiological traits. Changes to host aerobic metabolism are likely responsible for these parasite-induced performance alterations. Whole-organism metabolic rate is underpinned by cellular energy metabolism driven most prominently by the mitochondria. However, few studies have explored how mitochondrial enzymatic activity relates to body condition and parasite infection despite being a putative site for metabolic disruptions related to health status. We studied correlations among natural parasite infection, host body condition and the activity of key mitochondrial enzymes in target organs from wild-caught pumpkinseed sunfish ( Lepomis gibbosus ) to better understand the cellular responses of fish hosts to endoparasite infection. Enzymatic activities in the gills, spleen, and brain of infected fish were not significantly related to parasite infection or host body condition. However, the activity of cytochrome C oxidase, an enzyme involved in oxidative phosphorylation, in fish hearts was higher in individuals with lower body condition. Activities of citrate synthase, complexes I and III and carnitine palmitoyltransferase were also significantly different among organ types. These results provide preliminary information regarding the likely mitochondrial pathways affecting host body condition, the maintenance energetic requirements of different organs and their specific dependency on particular mitochondrial pathways. These results help pave the way for future studies on the effects of parasite infection on mitochondrial metabolism.