Matrix assisted laser desorption ionization-mass spectrometry imaging (MALDI-MSI) has become a powerful method to extract spatially resolved chemical information in complex materials. This study provides the first use of MALDI-MSI to define spatial-temporal changes in oil paints. Due to the highly heterogeneous nature of oil paints, the sample preparation had to be optimized to prevent molecules from delocalizing. Here, we present a new protocol for the layer-specific analysis of oil paint cross sections achieving a lateral resolution of 10 μm and without losing ionization efficiency due to topographic effects. The efficacy of this method was investigated in oil paint samples containing a mixture of two historic organic pigments, geranium lake and lead white, a mixture often employed in the work of painter Vincent Van Gogh. This methodology not only allows for spatial visualization of the molecules responsible for the pink hue of the paint but also helps to elucidate the chemical changes behind the discoloration of paintings with this composition. The results demonstrate that this approach provides valuable molecular compositional information about the degradation pathways of pigments in specific paint layers and their interaction with the binding medium and other paint components and with light over time. Since a spatial correlation between molecular species and the visual pattern of the discoloration pattern can be made, we expect that mass spectrometry imaging will become highly relevant in future degradation studies of many more historical pigments and paints.