Establishing relationships between parasite infection and physiological condition of the host can be difficult and therefore are often neglected when describing factors causing population declines. Using the parasite–host system between the parasitic nematode Contracaecum osculatum and the Eastern Baltic cod Gadus morhua, we here shed new light on how parasite load may relate to the physiological condition of a transport host. The Eastern Baltic cod is in distress, with declining nutritional conditions, disappearance of the larger fish, high natural mortality and no signs of recovery of the population. During the latest decade, high infection levels with C. osculatum have been observed in fish in the central and southern parts of the Baltic Sea. We investigated the aerobic performance, nutritional condition, organ masses, and plasma and proximate body composition of wild naturally infected G. morhua in relation to infection density with C. osculatum. Fish with high infection densities of C. osculatum had (i) decreased nutritional condition, (ii) depressed energy turnover as evidenced by reduced standard metabolic rate, (iii) reduction in the digestive organ masses, and alongside (iv) changes in the plasma, body and liver composition, and fish energy source. The significantly reduced albumin to globulin ratio in highly infected G. morhua suggests that the fish suffer from a chronic liver disease. Furthermore, fish with high infection loads had the lowest Fulton’s condition factor. Yet, it remains unknown whether our results steam from a direct effect of C. osculatum, or because G. morhua in an already compromised nutritional state are more susceptible towards the parasite. Nevertheless, impairment of the physiological condition can lead to reduced swimming performance, compromising foraging success while augmenting the risk of predation, potentially leading to an increase in the natural mortality of the host. We hence argue that fish–parasite interactions must not be neglected when implementing and refining strategies to rebuild deteriorating populations.