The use of indirect calorimetry is strongly recommended to guide nutrition therapy in critically ill patients, preventing the detrimental effects of under- and overfeeding. However, the course of energy expenditure is complex, and clinical studies on indirect calorimetry during critical illness and convalescence are scarce. Energy expenditure is influenced by many individual and iatrogenic factors and different metabolic phases of critical illness and convalescence. In the first days, energy production from endogenous sources appears to be increased due to a catabolic state and is likely near-sufficient to meet energy requirements. Full nutrition support in this phase may lead to overfeeding as exogenous nutrition cannot abolish this endogenous energy production, and mitochondria are unable to process the excess substrate. However, energy expenditure is reported to increase hereafter and is still shown to be elevated 3 weeks after ICU admission, when endogenous energy production is reduced, and exogenous nutrition support is indispensable. Indirect calorimetry is the gold standard for bedside calculation of energy expenditure. However, the superiority of IC-guided nutritional therapy has not yet been unequivocally proven in clinical trials and many practical aspects and pitfalls should be taken into account when measuring energy expenditure in critically ill patients. Furthermore, the contribution of endogenously produced energy cannot be measured. Nevertheless, routine use of indirect calorimetry to aid personalized nutrition has strong potential to improve nutritional status and consequently, the long-term outcome of critically ill patients.