The study of mortuary practices in Mainland and Island Southeast Asia has revealed complex and diverse treatments of the deceased. From secondary to flexed and seated internments during the Pleistocene, to the emergence of extended burials in the mid-late Holocene, Mainland and Island Southeast Asia are unique geographic settings that enable us to explore changes and continuation in burial practices. This paper contributes to this topic with the description of three new burials excavated in Tron Bon Lei (Alor Island, Indonesia) dated to 7.5, 10, and 12 kya cal BP. In addition to the bioskeletal profiles and palaeohealth observations, we propose the adoption of archaeothanatological methods to characterise burial types in the region. Through the analysis of skeletal element representation, body position, articulation, and grave associations, we provide an example of a holistic approach to mortuary treatments in the Lesser Sunda Islands. Our results provide significant new data for understanding the evolution and diversification of burial practices in Southeast Asia, contributing to a growing body of literature describing prehistoric socio-cultural behaviour in this region.