Morphometric indices of body condition are assumed to reflect an animal’s health and ultimately its fitness, but their physiological significance remains a matter of debate. These indices are indeed usually considered as proxies of energy reserves, ignoring other physiological processes involved in animal health such as nutritional, immune and hormonal states. Given the wide variety of ecological processes investigated through morphometric body condition indices in marine sciences, there is a clear need to determine whether morphometric indices reflect primarily individuals’ energy reserves or their broader integrated physiological status. To address this issue, we used morphometric and physiological data (cortisol level, oxidative stress, digestive enzymes activity, and both fatty acids percentage and total amount) collected in three stocks of the European sardine (Sardina pilchardus) presenting contrasted patterns of growth and body condition. We found that morphometric body condition indices are indeed mainly and consistently linked to a proxy of the amount of lipid reserves (i.e., fatty acids amount), but also significantly to quality of lipid reserves (i.e., fatty acids percentage) and fish chronic stress (scale cortisol levels). We found no significant relationship between morphometric indices of body condition and both oxidative stress proxies and variables measuring digestive enzymes activity. Our study confirmed that morphometric body condition indices primarily reflect the variance in individuals’ lipid reserves and to a lesser extent the actual composition of these reserves (linked to differences in fish diet) and scale cortisol levels (indicating fish metabolism and/or their chronic stress levels). Therefore, some non-energetic aspects should be considered when studying individuals’ responses to environmental changes and other key physiological processes (oxidative stress proxies, activity of digestive enzymes) should be investigated directly to support scientific-based decision-making in the context of climate change.