This paper discusses the pros and cons of the application of automated SEM-EDS analysis to the characterization of pottery findings by means of a thorough discussion of the basics of its technology as well as its use in archaeometric research. An in-depth investigation of coarse prehistoric pottery (42 thin sections) from the Petit-Chasseur necropolis (3100-1600 BC, Southwestern Switzerland) provided the perfect testing ground for automated SEM-EDS analysis and resulted in a complete and updated reflection on the capabilities and limitations of this method. An opportunity to produce a quick, reliable, automated, and in-depth petrographic characterization of archaeological ceramics in the form of detailed phase maps stands as a unique feature of automated SEM-EDS technology. Indeed, the information on the composition of aplastic inclusions and clayey groundmass along with the insights on void distribution offer a great resource enabling inferences on raw material choices/provenance and manufacturing technology. However, the present study exposed there are more disadvantages than the ones reported by the literature. A phase identification ignoring crystallographic particularities whatsoever is potentially alarming for mineral sorting, whereas the simplification of lithoclast’s internal texture hampers the lithological classification of aplastic inclusions. Notwithstanding listed limitations, the use of automated SEM-EDS in archaeometric research of pottery offers a wealth of useful data which will secure its place in any future investigation of archaeological materials, alongside with the more traditional techniques such as optical petrography, regular scanning electron microscopy and X-ray diffraction.