Dental caries is the most prevalent chronic infectious disease during childhood both in historical and contemporary times, but research focused on the oral health of non-adults from the past is still scant. As such, this study proposes a multidisciplinary approach to the differential diagnosis of severe dental lesions in a medieval non-adult skeleton. The skeleton of a three-year-old child recovered in the medieval necropolis of Cacela Velha (Portugal) was studied through macroscopic, radiological, elemental and stable isotope analyses. This individual exhibited enamel destruction and dentine exposure in both the maxillary and mandibular teeth, with the latter also showing changes in coloration. Elemental analysis showed that his skull presented lower values of Si, Cl, and Ca and higher of Cu compared to the control, while the concentration of P and S were significantly lower in the teeth. Early childhood caries is the most probable diagnosis for the dental lesions observed, apparently stemming from a reticulate of factors that include potential malnutrition, and the consumption of sugars in complementary feeding - even though historical sources point to the scarcity of sugar in Portugal during most of the Middle Ages.