The Australian-Indonesian monsoon (AIM) system is an important determinant of the climate system in the tropical Indo-Pacific region. The factors controlling past variability of the AIM are, however, less well understood. Here, we present 2000 years high-resolution records of Australian-Indonesian winter monsoon (AIWM) winds and summer monsoon (AISM) rainfall from the same sedimentary archive retrieved offshore southern Indonesia. AIWM winds were generally strong during the Little Ice Age (LIA) and weak during the Medieval Warm Period (MWP) and the Roman Warm Period (RWP). We find that rainfall was generally stronger during the LIA and weaker during the MWP and RWP. Based on modern instrumental records, we suggest that changes in the background state of the tropical Pacific so-called El Niño-like or La Niña-like conditions may have substantially contributed to the multi-decadal and centennial-scale upwelling variations and hence changes in austral winter monsoon winds over the past 2000 years. However, the prevalence of El Niño-like conditions during the LIA and La Niña-like conditions during the MWP and RWP conflicts with our AISM rainfall reconstructions. It is expected from modern observations that periods of more frequent and/or intense El Niño events, such as during the LIA have resulted in reduced rainfall and subsequent drought in the AISM region and, consequently, less riverine terrestrial supply to our site. This disagreement might suggest that either the centennial-scale variations of the AISM and AIWM during the past 2000 years are unrelated to ENSO dynamics and other factors, such as variations in the strength of the Walker circulation need to be invoked to explain austral summer and winter monsoon variability, or that El Niño events co-vary with La Niña events on that time scales, which typically would result in increased rainfall over central and southern Indonesia and northern Australia.