PIXE and EBS were used simultaneously to characterize paint layers containing pigments of controlled grain size. The experiments were carried out using the external 3 MeV proton beam from the NewAGLAE facility. The paint layers consisted of lead silicate pigments mixed in linseed oil. The pigments were characterized by XRD and SEM prior to IBA measurements. Irregularly shaped grains ranging from 13 to 64 µm were observed. The PIXE spectra were fitted by TRAUPIXE and the EBS spectra were simulated with STRUCTNRA using simplified models of the paint structure assuming non-overlapping spherical pigment particles in oil. For each simulation, the particle size was used as provided by the SEM observations. The density of each paint layer was calculated according to the pigment composition determined by PIXE. For the linseed oil matrix, the oxygen content was fitted at about two times higher than in linseed oil, which is qualitatively consistent with the oxygen uptake during the drying process. The pigment volume fraction and the stick-out fraction were adjusted to fit the experimental spectra. A reasonable agreement between experimental and simulated spectra was achieved. This demonstrates that the simulation and quantitative understanding of EBS spectra from paintings requires the microstructure of the paint layer to be taken into account.