This paper details the results of analyses of animal remains recovered from the excavations of Song Gupuh, a rockshelter in Eastern Java’s Gunung Sewu region, presumably occupied by hunter-gatherers from ca. 30,000 to 5000 years ago. The Late Pleistocene assemblage of the site is dominated by large mammals including cervids and bovids, whereas the Early to Mid-Holocene deposits yielded evidence for targeted hunting/trapping of smaller mammals, most notably leaf monkeys. Taphonomic analyses, including bone fragmentation patterns and surface modifications, allowed us to characterize the nature of occupation in the rockshelter at different time periods. We applied dental microwear analyses on bovid and cervid teeth, as well as carbon and oxygen stable isotope studies of dental enamel of numerous animal taxa to gain insights into changes in the local environment. We demonstrate that an increase in rainforest cover following the onset of the Holocene did not result in the complete disappearance of grasslands. We synthesized our findings with results on faunal assemblages from contemporaneous, nearby sites in the East Java, and situate them in the burgeoning zooarchaeological literature for Late Pleistocene hunter-gatherers in South/Southeast Asia.