The issue of preserving carbonatic stones of cultural heritage (CH) restored in the past that have undergone new decay phenomena is strongly emerging and conservation science has not yet found a reliable solution. In this paper, we propose the application of synchrotron radiation X-ray diffraction computed tomography (XRDCT) to explore the effects of using inorganic-mineral products (ammonium oxalate; ammonium phosphate) in sequence as a novel, compatible and effective re-treatment approach to consolidate decayed carbonatic stones already treated with inorganic-mineral treatments. High-quality XRDCT datasets were used to qualitatively/quantitatively investigate and 3D localize the complex mixture of crystalline phases formed after the conservation re-treatments within a porous carbonatic stone substrate. The XRDCT reconstruction images and the structural refinements of XRD patterns with the Rietveld methods showed that the phase composition of reaction products, their volume distribution, and weight fraction vary as a function of the treatment sequence and penetration depth. The high potential of XRDCT allows (i) assessment of peculiar trends of each treatment/treatment sequence; (ii) exploration of the reaction steps of the sequential treatments and (iii) demonstration of the consolidating effect of inorganic re-treatments, non-destructively and at the micron scale. Above all, our study (i) provides new analytical tools to support the conservation choices, (ii) showcases new analytical possibilities for XRDCT in conservation science, including in investigations of CH materials and decay processes, and (iii) opens up new perspectives in analytical chemistry and material characterisation for the non-destructive and non-invasive analysis of reactions within heterogeneous polycrystalline systems.