Dynamic Energy Budget (DEB) models rely on measurements of food availability to describe the rates at which organisms assimilate and use energy from food for maintenance, growth, maturation and reproduction. Although crucial, the determination of appropriate and accurate energy input variables can be problematic. We developed an inverted DEB model to reconstruct the food intake from temperature and growth trajectories. The method makes use of a reformulation of the DEB model dynamics into a second order linear equation. This formula not only allows the reconstruction of the scaled functional response but also gives access to reserve dynamics, mobilization, and somatic maintenance fluxes. The shell of the great scallop, Pecten maximus, providing high resolution records of incremental growth, was used to explore the potential of this approach to reconstruct the functional response from daily shell growth rates data. In a theoretical case, we investigated the resolution and sensitivity limits of the method. In a validation process, predictions were used to re-simulate growth that was compared to the initial growth trajectory. Moreover, as growth data used in the reconstruction process usually show high-frequency variability, we also developed a smoothing method, based on DEB theory assumptions, to filter growth data time series.