We analyze injuries in the cranial sample from the Pucará de Tilcara fortress, dating to the time of the Inca conquest. Analysis of violence markers, carried out by visual examination and computed tomography, and the comparison of results with those relating to samples from the Regional Development Period of the Quebrada de Humahuaca valley, suggest that although the violence level remained high, its nature could have changed after the arrival of the Inca. The female sample reveals just two perimortal injuries, no trophy skulls were found, and the frequency of nasal bone fractures is higher than in earlier samples. This may indicate lower level of between-group fighting for control over resources, and higher risk of interpersonal violence. The observed pattern suggests that having arrived in the Quebrada de Humahuaca region, the Inca eased political tension by establishing control over trade routes and the distribution of arable land areas, which had previously been the main cause of local armed clashes. The influence of artificial cranial modifications on the pathological and traumatic status of individuals was also analyzed. Two types of modification were recorded in the sample-fronto-occipital tabular oblique and fronto-occipital tabular straight. None of them caused pathological changes or a decrease in the thickness of cranial bones.