During the highly dynamic, climate-driven Pleistocene period, mammalian communities from the Indomalayan region faced major environmental changes. In the late Middle to the Late Pleistocene, the Sunda Shelf surface was particularly affected under the influence of multiple parameters—tectonic, eustatic and climatic—leading to alternating phases of exposure and flooding. The fossil faunas from the Padang Highlands in Sumatra discovered by Eugène Dubois illustrate episodes of species dispersal during the periods of exposure of land areas. Here, we analyse the assemblages of Sibrambang and Lida Ajer in the light of a selection of mammalian faunas located in continental and insular regions during two possible periods of dispersion, c. 130 ka at the Marine Isotope Stage (MIS) 6–5 transition and c. 71 ka at the beginning of MIS 4. We investigated (1) the taxonomic composition of herbivore communities in terms of archaic versus modern taxa; (2) the functions of ecosystems, based on the type of digestive physiology of herbivores (ruminant versus non-ruminant) per body mass category; and (3) the relative abundance of some Artiodactyla, Perissodactyla and Primates. Our results show that, at the time of the earliest range expansion of modern species into Sundaland c. 130 ka, diverse functional herbivore communities containing local archaic taxa coexisted in Southeast Asia. Overall, Sundaland seems to have always been less rich in large-bodied herbivore diversity compared to the Indochinese subregion, most probably reflecting the lower heterogeneity of Sundaic ecosystems, even during the period of large connections between land masses. By comparing Duoi U’Oi, Vietnam (Homo sp.; 70–60 ka) and Lida Ajer, Sumatra (Homo sapiens; 73–63 ka), two sites located at different latitudes, the results underscore the different availability to humans of herbivore prey species depending on their relative abundance in highly forested habitats.