This work shows the benefits of characterizing historic paintings via compositional and microtextural data from micro-X-ray diffraction (μ-XRD) combined with molecular information acquired with Raman microscopy (RM) along depth profiles in paint stratigraphies. The novel approach was applied to identify inorganic and organic components from paintings placed at the 14th century Islamic University-Madrasah Yusufiyya-in Granada (Spain), the only Islamic University still standing from the time of Al-Andalus (Islamic Spain). The use of μ-XRD to obtain quantitative microtextural information of crystalline phases provided by two-dimensional diffraction patterns to recognize pigments nature and manufacture, and decay processes in complex paint cross sections, has not been reported yet. A simple Nasrid (14th century) palette made of gypsum, vermilion, and azurite mixed with glue was identified in polychromed stuccos. Here also a Christian intervention was found via the use of smalt, barite, hematite, Brunswick green and gold; oil was the binding media employed. On mural paintings and wood ceilings, more complex palettes dated to the 19th century were found, made of gypsum, anhydrite, barite, dolomite, calcite, lead white, hematite, minium, synthetic ultramarine blue, and black carbon. The identified binders were glue, egg yolk, and oil.