Archaeological and palaeoenvironmental investigations at Juukan 2 rockshelter have yielded new information on the ancient Aboriginal occupation of the Pilbara uplands in northwest Australia. Using multiple lines of evidence, including lithic, faunal, pollen, ancient DNA, radiocarbon dating, optically stimulated luminescence, and Bayesian chronological modelling, we show that Aboriginal people occupied the western Hamersley Plateau as early as 47,000 years ago (47 ka). Late Pleistocene populations utilised a diverse range of tool technologies, including bone points, grindstones, and flaked stone artefacts. Palaeoclimatic conditions at Juukan 2 rockshelter varied greatly over the past 47 ka, with repeated site visits by people, including during the peak hyper-arid phase of the Last Glacial Maximum (LGM) c. 21 ± 2 ka. Ancient starch analyses of the ground stone artefacts show the processing of Ipomoea (Bush Potato) from around 42 ka to the present day. Pronounced increases in the discard of stone artefacts and bone in the last 3500 years are interpreted to be the result of increased frequency of site use. A braided hair fragment dated to this period has demonstrated genetic links between the earlier rockshelter occupants and contemporary Puutu Kunti Kurrama and Pinikura peoples, who have maintained strong cultural connections to the area.