Up to now, among the IBA techniques, only PIXE has been used for analyzing paintings. However, quantitative PIXE analysis is sometimes difficult to interpret due to the layered structure, the presence of varnish and organic binder and, in some cases, discoloration of the pigments has been observed due to the interaction of the ion beam with the compounds. In order to improve the characterization of paintings, we propose some alternative experimental procedures. First of all, backscattering spectrometry (BS) and PIXE are simultaneously combined in order to collect complementary information such as layer thickness and organic compound quantification. The simultaneous PIXE and BS experiments also have the advantage of being able to analyze the same area in one experiment. This combination, implemented with an external beam, was directly applied on paintings and on painting cross-sections for the study of Italian Renaissance masterpieces. We have obtained valuable results not only on the pigment itself but also, for the first time, on the binder to pigment proportion which is not well documented in the ancient recipes. Moreover, in order to restrain beam damages due to the ion stopping power, we propose to analyze very thin painting cross-sections by a combination of PIXE–RBS and Scanning Transmission Ion Microscopy (STIM).