The study of the alteration process, and in particular of secondary phases precipitated in pottery after its production, can constrain the post-depositional environments or the type of use of the pottery. Detailed study of secondary phases can be done using different approaches, based on microscopic, microstructural and microchemical analyses, as well as mineralogical methods. In the present study are reported the results of the application of punctual mineralogical analysis by synchrotron through-the-substrate microdiffraction (tts-μXRD) to analyse secondary phases precipitated in ancient pottery (Bronze Age pottery form Frattesina in Italy and Mesolithic pottery form Al Khiday in Sudan). Although the chemical composition of these secondary phases in many cases almost matches with the stoichiometric composition of a known mineral, only some of them were actually true mineral phases (i.e. with crystallinity and therefore showing diffraction peaks), while others were amorphous. Some phases, the occurrence of which was previously attested only on the basis of their chemical composition (determined by scanning electron microscope or the electron microprobe analysis), were univocally identified as true vivianite (Fe(PO)·8HO) and crandallite (CaAl(PO)(OH)·HO) minerals. Part of the phases detected in studied pottery, the chemical composition of which was consistent with specific mineral phases, were instead amorphous. The synchrotron through-the-substrate microdiffraction (tts-μXRD), therefore, represents a valid method for properly determine the mineralogical nature of secondary phases in pottery, as well as other small-sized and rare mineral phases occurring in polycrystalline materials of archaeological interest, such as pottery, mortars, painting and glassy materials.