Isotopes of strontium, oxygen, and carbon were analyzed in human tooth enamel from two Postclassic sites in the central Peten lakes region, Guatemala, to examine patterns of mobility and diet during a time of social unrest. Excavations at both sites, Ixlu and Zacpeten, have revealed evidence for purposeful dismemberment and interment of individuals. This study examines a possible shrine surrounded by rows of skulls at Ixlu, and a mass grave of comingled individuals interred at Zacpeten. The interments coincide with a period of conflict and warfare between two dominant polities, Itza and Kowoj. The 14 sampled individuals at Ixlu were young males, six of whom isotopically match the Maya Mountains of central Belize/southeastern Peten. At Zacpeten, isotopic signatures of adults and children (n = 68) suggested that many were either local or came from other parts of the Maya lowlands, but not the Maya Mountains. In the Late Postclassic, the Zacpeten individuals were exhumed, defiled, and deposited in a mass grave, probably by Kowojs. Although temporally and geographically related, the Ixlu and Zacpeten burials represent two distinct cases of ritual violence that reflect the tumultuous political landscape of the Postclassic period.