This paper investigates the effect of the paint layer used for infrared thermography on the heat source estimation for thin plates. The thermal behaviour of two plates is studied using finite element modelling. The first one is composed of the studied homogeneous material. The second one is a sandwich plate composed of a central material covered on each side with a high emissivity paint layer. For the two plates, two thermal loading cases are simulated. Case 1 corresponds to natural cooling from a initial uniform temperature to room temperature. Case 2 corresponds to a situation where the initial uniform temperature is equal to room temperature. In both cases, the central material is loaded with internal heat sources leading to temperature field variation. From the computed external surface temperature, heat sources and energy are then estimated using homogeneous plate and sandwich plate models derived from the heat diffusion equation. Then, the estimated heat sources are compared to the one input in the finite element model. It is shown that the paint layer significantly isolates the central material from the external environment. In case 1, it is shown that the error is reduced from 10% with the homogeneous plate model to 5%, with the sandwich plate model. In case 2, heat sources are estimated with an error of less than 8% with the homogeneous plate model while it is below 2% with the sandwich plate model. The sandwich plate model is thus significantly more accurate for heat source and energy estimations than the homogeneous plate model.