Pottery is a complex archaeological material that is found ubiquitously in various spatial—temporal frameworks from all over the world; therefore, it is of great importance to archaeological research. The current paper aims to present and discuss the results obtained on a batch of Neolithic (ca. 6000–5000 BC) and Chalcolithic (ca. 5000–3900 BC) pottery sherds from Southern Romania through X-ray Computed Tomography, a non-destructive methodology that allows for the 3D reconstruction and precise measurement of inclusions and voids present within ceramic artefacts. Images from several potsherds were subsequently exported and analyzed by means of dedicated software (ImageJ 1.54p and GIMP) to extract quantitative information on the observed features. Grain size and morphometric analyses were performed on the particles, while the contour variability of the examined inclusions was characterized through the application of shape descriptors. Voids were analyzed in order to reveal specific orientation patterns through the examination of the aspect ratio of the holes and of the Rayleigh z test values. These analyses evidenced the general reliance of moderately and poorly sorted clays for ceramic production, accompanied by a gradual transition from organic to grog tempering, while conservative traditions remained prevalent in primary pottery-forming processes.