Indirect calorimetry (InCa) estimates whole-body energy expenditure and total substrate oxidation based on O
2
consumption and CO
2
production, but does not allow for the quantification of oxidation of exogenous substrates with time. To achieve this, we incorporated
13
CO
2
and
12
CO
2
gas sensors into a commercial InCa system and aimed to demonstrate their performance and added value. As a performance indicator, we showed the discriminative oscillations in
13
CO
2
enrichment associated with food intake in mice fed diets containing naturally low (wheat)
vs
high (maize)
13
C enrichment. To demonstrate the physiological value, we quantified exogenous
vs
total carbohydrate and fat oxidation continuously, in real time in mice varying in fat mass. Diet-induced obese mice were fed a single liquid mixed meal containing
13
C-isotopic tracers of glucose or palmitate. Over 13 h, ~70% glucose and ~48% palmitate ingested were oxidised. Exogenous palmitate oxidation depended on body fat mass, which was not the case for exogenous glucose oxidation. We conclude that extending an InCa system with
13
CO
2
and
12
CO
2
sensors provides an accessible and powerful technique for real-time continuous quantification of exogenous and whole-body substrate oxidation in mouse models of human metabolic physiology.