The assessment of the penetration depth of conservation treatments applied to cultural heritage stone materials is a burning issue in conservation science. Several analytical approaches have been proposed but, at present, many of them are not fully exhaustive to define in a direct way the composition and location of the conservation products formed after inorganic mineral treatments. Here, we explored, for the first time, the analytical capability of synchrotron radiation μ X-ray diffraction in transmission geometry (SR-μTXRD) for the study of the crystal chemistry and penetration depth of the consolidating phases formed after the application of diammonium hydrogen phosphate (DAP) treatments on a porous carbonatic stone (Noto limestone). The SR-μTXRD approach provided unambiguous information on the nature of the newly formed calcium phosphates (hydroxyapatite, HAP, and octacalcium phosphate, OCP) with depth, supplying important indications of the diffusion mechanism and the reactivity of the substrate. Qualitative and semi-quantitative data were obtained at the microscale with a non-destructive protocol and an outstanding signal-to-noise ratio. The SR-μTXRD approach opens a new analytical scenario for the investigation of a wide range of cultural heritage materials, including natural and artificial stone materials, painted stratigraphies, metals, glasses and their decay products. Furthermore, it can potentially be used to characterize the penetration depth of a phase "A" (or more crystalline phases) in a matrix "B" also beyond the cultural heritage field, demonstrating the potential wide impact of the study.