Fluorescence analysis of materials used as binders and coatings in artworks is often hampered by numerous factors, leading to uncertainties in data interpretation. Fluorescence lifetime (FL) measurements enable improvement of the specificity with respect to steady-state measurements by resolving the decay dynamics of the fluorophore emissions. In this work, layers of natural resin, oil, and wax—in pure form, pigmented, in mixtures, and spread on different substrates—were analyzed using a compact, portable, fiber-based FL instrument. FL data were processed via the phasor method and integrated with Raman spectroscopy to obtain complementary chemical information on the different substances. It was observed that the τ-phase of the mixtures is affected by both the pigments and the dispersing medium, and that the presence of the metal substrate contributes to changes in the FL of mixtures. The results obtained with our portable FL system combined with Raman spectroscopy pave the way for a systematic study of a larger number of materials for future in situ applications on works of art.