We report the development of innovative embedding procedures for the analysis of paint cross sections by attenuated total reflection (ATR) Fourier transform IR microscopy. This technique was chosen because it is widely employed for the characterization and spatial location of organic and inorganic components in artistic samples. Moreover, the performance of the technique may be critically affected by sample preparation in terms of surface morphology and the presence of contamination. First, we evaluated the use of KBr as a barrier to contamination by the embedding synthetic medium. In this way, the sample cross section can be polished by means of a sample holder, which allows a controlled pressure to be applied to the sample, thus improving the reproducibility and quality of the surface cross section. In addition, argon ion milling was used for the polishing of samples embedded in KBr, and provided very promising results in terms of surface planarity and reduction of superficial contamination by KBr. Finally, the use of NaCl as an alternative to KBr was proposed thanks to its advantages in terms of hygroscopicity, cost, and toxicity. In addition, cross sections embedded in NaCl were characterized by greater hardness, a feature that allowed us to obtain improved contact with the ATR crystal.