In recent decades, East Borneo has become an increasingly important archaeological “hot-spot” in Island Southeast Asia as a result of early dates for rock art ca. 38,000 BP and the greater number of excavated sites that support a much longer period of human occupation. However, the chronology of settlement and adaptation to environmental changes during the Pleistocene–Holocene transition is still poorly known. Here we report on an excavation at the Liang Abu rock shelter which has contexts dating from the Late Pleistocene (12,660 ± 58 uncal. BP) to the present day, indicating a terminus ante quem (TAQ) for human occupation at 23,790 BP. We present the results of an attempt to systematically integrate and compare data from Liang Abu and Kimanis, a geographically close site with a previously published sequence. Particular attention is paid to post-depositional issues in tropical settings and to data compatibility, reuse, and reproducibility, relying on open-source software for data processing (R scripts) and Bayesian chronological modeling. Two Bayesian models are built and compared using the ChronoModel software, which can handle outliers and uncertainty (e.g., freshwater reservoir effect). This first inter-site comparison for Borneo results in a new chronology of human settlement and mainland–coastal interactions in East Borneo and paves the way for future regional synthesis.