This work deals with the identification of natural binders and the study of the complex stratigraphy in paintings using reflection FT-IR spectroscopy, a common diagnostic tool for cultural heritage materials thanks to its non-invasiveness. In particular, the potential of the near-infrared (NIR) spectral region, dominated by the absorption bands due to CH, CO, OH and NH functional groups, is successfully exploited to distinguish a lipid binder from a proteinaceous one, as well as the coexistence of the two media in laboratory-made model samples that simulate the complex multi-layered structure of a painting. The combination with multivariate analysis methods or with the calculation of indicative ratios between the intensity values of characteristic absorption bands is proposed to facilitate the interpretation of the spectral data. Furthermore, the greater penetration depth of NIR radiation is exploited to obtain information about the inner layers of the paintings, focusing in particular on the preparatory coatings of the supports. Finally, as proof of concept, FT-NIR analyses were also carried out on six paintings by artists working in Lombardy at the end of the 15th century, that exemplify different pictorial techniques.