We report the results of a test excavation of deposits in a limestone cave sub-chamber located beneath the main chamber of Liang Bua, Flores, Indonesia; the discovery site of the small hominin species, Homo floresiensis. Well-preserved remains of extinct Pleistocene fauna and stone artefacts have previously been identified on the surface of a sediment cone within the sub-chamber. Our excavation of the deposits, at the base of the sediment cone in the sub-chamber (to 130 cm depth) yielded only a few fragmentary bones of extant fauna. Uranium/Thorium (U-series or U/Th) dating of soda straw stalactites excavated from 20 to 130 cm in depth demonstrates that the excavated sediments were deposited during the Holocene. Red Thermoluminescence (TL) dating of the sediments at the base of the excavation (130 cm depth) indicates these sediments were last exposed to sunlight at 84 ± 15 ka (thousand years), similar to red TL ages of cave sediments from the main chamber. Together, these results indicate that the surface faunal remains, which are morphologically analogous to Pleistocene finds from the main chamber excavations, were transported to the sub-chamber relatively recently from the main chamber of Liang Bua and probably originated from conglomerate deposits at the rear of the cave and from deposits around the front entrance. There is no evidence for hominin occupation of the sub-chamber, instead it seems to have acted as a sink for cultural materials and fossil remains transported from the surface via sinkholes. Despite the small number of finds from the test excavation, it is possible that more extensive excavations may yield additional transported cultural and faunal evidence at greater depths.