In cultural heritage, paint stratigraphies are complex systems typically consisting of various paint layers with fine crystalline phases mixed with coarse pigment and filler grains. This complexity poses significant challenges for X-ray diffraction (XRD) analysis. In this work, we employed synchrotron radiation micro-X-ray diffraction in transmission geometry (SR-µTXRD) with linear mapping to develop a novel approach for studying the crystalline phases (pigments and fillers) in mock-up paint stratigraphies. A targeted approach was followed for qualitative, quantitative, and microstructural analysis, combining signals from micrometric crystallites and coarse single crystals as well as from randomly oriented and iso-oriented crystalline phases. This allows for identifying, localizing, and quantifying these phases even in low fractions and distinguishes the same phases across different layers with varying grain sizes or spatial orientations. Critical analysis of 2D XRD patterns, coupled with full-profile fitting performed by the Rietveld method, provides insights into material preparation (e.g., grinding), painting technique (e.g., color palette, use of fillers, brushing), and crystallo-chemical modifications over time. This analytical approach, integrating spatially resolved investigation with high-quality phase characterization, enhances the potential of specific XRD methodologies for a 2D investigation of multi-phase materials in cultural heritage, even without dedicated micro-mapping techniques.