Abstract This study assesses the prevalence and distribution of caries, antemortem tooth loss, abscesses, calculus, alveolar bone resorption, and tooth wear in two large composite archaeological series from Croatia in order to determine the effects that long‐term, endemic warfare had on dental health and nutrition. The first series consists of dental material belonging to three cemeteries dated to the late medieval period (1100–1400), a period characterised by rapid social development, increased urbanisation, growth of trade, and an increase of monetary economy. The second belongs to three cemeteries from the early modern period (1400–1700) during which time Croatia was exposed to incessant Ottoman raiding and the gradual subjugation and incorporation of various Croatian territories into the Ottoman Empire. Analyses of 4,789 permanent teeth belonging to adult males and females show significantly lower frequencies of carious lesions, abscesses, alveolar resorption, and heavy dental wear during the early modern period suggesting a significant change in alimentary habits with, surprisingly, better nutrition and a higher dependence on proteins during the period that Croatia was involved in low‐intensity, endemic warfare. The improvement in dental health noted in the Ottoman period series was the result of a combination of circumstances that includes mass emigration of local populations caused by incessant Ottoman raiding, the resulting economic decline and wholesale abandonment of these territories, and the subsequent resettlement of these territories by a new group of peoples known as Vlachs who practised a different subsistence strategy based on pastoralism and cattle farming.