Official URL: https://doi.org/10.1038/s41598-022-21843-8

Antiphase behaviour of monsoon systems in alternate hemispheres is well established at yearly and orbital scales in response to alternating sensible heating of continental landmasses. At intermediate timescales without a sensible heating mechanism both in-phase and antiphase behaviours of northern and southern hemisphere monsoon systems are recorded at different places and timescales. At present, there is no continuous, high resolution, precisely dated record of millennial-scale variability of the Indonesian–Australian monsoon during the last glacial period with which to test theories of paleomonsoon behaviour. Here, we present an extension of the Liang Luar, Flores, speleothem δ18O record of past changes in southern hemisphere summer monsoon intensity back to 55.7 kyr BP. Negative δ18O excursions (stronger monsoon) occur during Heinrich events whereas positive excursions (weaker monsoon) occur during Dansgaard-Oeschger interstadials—a first order antiphase relationship with northern hemisphere summer monsoon records. An association of negative δ18O excursions with speleothem growth phases in Liang Luar suggests that these stronger monsoons are related to higher rainfall amounts. However, the response to millennial-scale variability is inconsistent, including a particularly weak response to Heinrich event 3. We suggest that additional drivers such as underlying orbital-scale variability and drip hydrology influence the δ18O response.