Understanding mechanisms affecting the renewal of populations is critical for species’ conservation and living resources management. For fish species, density-dependant mechanisms occurring in young stages are particularly well studied. The food limitation hypothesis assumes that the food availability is the main limiting factor for juveniles’ growth and survival in coastal and estuarine nurseries. Although some promising modelling methods appeared to test this hypothesis, it remains debated because of a lack of a clear signal of food limitation. We use a mechanistic approach based on DEB (Dynamic Energy Budget) theory to test the trophic limitation hypothesis from a metabolic point of view. The energy intake of individuals is quantified given the experienced temperatures, and measures of individuals’ length-at-age. We reconstruct the food ingested in an “inverse”-DEB modelling. Then, we further explore the potential of inverse-DEB modelling to describe in fine details the energy partitioning between the main metabolic processes (i.e., maintenance, maturation and growth) of an individual, and highlight periods of energy shortage indicating a trophic limitation. As a case study, we implemented this approach for the juveniles of common sole (Solea solea) settled between 2000 and 2014 in the Seine estuarine nursery. Our approach allowed to (i) quantify food assimilation, and identify (ii) a decrease in the growth efficiency, and (iii) the occurrence of nutritional stress. Both the decrease in growth and the periods of nutritional stress coincide with a decrease in individual-specific food availability. Therefore, the inverse-DEB approach is an interesting tool to test the food limitation hypothesis at the individual scale. DEB theory deepens and structures our knowledge on energy intake and energy use, hence suggesting concrete indices of trophic limitation such as periods of non-growing, and nutritional stress due to starvation (i.e. no food intake). Work on the parametrization of the DEB model is progressing rapidly and our method can already be generalized to other fish species. Finally, mechanistic description of food limitation using bioenergetic modelling helps better understanding the ecology of the species in a dynamic environment. This may ultimately help going towards better species’ conservation and fisheries management.