A prototypical in situ noninvasive study of ancient mural painting materials has been carried out using an easily manageable fiber-optic Fourier transform mid-infrared (mid-FT-IR) reflectance spectrophotometer. The reported object of the study is the Renaissance fresco by Pietro Vannucci, called il Perugino, located in the church of Santa Maria delle Lacrime (1521, Trevi, Perugia Italy). For the first classification and interpretation of infrared spectra, principal components analysis was used. Spectral artifacts due to lacunas, restoration materials, or alteration products have been identified, as well as two different secco refinements bound in a tempera medium. For the characterization of inorganic pigments, mid-FT-IR spectra have been integrated with other data obtained through in situ X-ray fluorescence (XRF) elemental analysis. This complementary noninvasive approach led to the characterization of Perugino's pigments, even in the presence of complex mixtures. The mid-FT-IR noninvasive technique, in combination with XRF, is thus recommended as a valuable first approach for the examination of mural paintings, permitting the assessment of the execution technique as well as contributing to the evaluation of the conservation state.