We present an overview of recent advances in the application of Fourier Transform Infrared (FTIR) microscopy for analysis of complex, multicomponent, and multilayer samples such as those typically encountered in the field of heritage materials. This technique is particularly useful since it allows identification and localization of both organic and inorganic (if IR active) compounds. New improvements have been possible thanks to the introduction of ad hoc sample preparation methods to obtain either thin or cross sections that allow both avoidance of contamination from organic embedding resin and improvement of the quality of the acquired spectra. Moreover, integrated use of spectra registered in the near-infrared (NIR) and mid-infrared (MIR) regions allows better comprehension of cross section composition. Data interpretation has been improved thanks to the development of chemometric methods for elaboration of hyperspectral data. A new and very promising field is the development of enhanced FTIR methods for detection of trace components in microextracts. These systems, allowing detection of extractable organic compounds from about 0.1 mg of sample, will be extremely useful in the future for analysis of natural and synthetic colorants, varnishes extracted, for instance, from cotton swabs used during cleaning of paintings, and organic residues on archeological remains.