The Indian Ocean Dipole (IOD)--an oscillatory mode of coupled ocean-atmosphere variability--causes climatic extremes and socio-economic hardship throughout the tropical Indian Ocean region. There is much debate about how the IOD interacts with the El Niño/Southern Oscillation (ENSO) and the Asian monsoon, and recent changes in the historic ENSO-monsoon relationship raise the possibility that the properties of the IOD may also be evolving. Improving our understanding of IOD events and their climatic impacts thus requires the development of records defining IOD activity in different climatic settings, including prehistoric times when ENSO and the Asian monsoon behaved differently from the present day. Here we use coral geochemical records from the equatorial eastern Indian Ocean to reconstruct surface-ocean cooling and drought during individual IOD events over the past approximately 6,500 years. We find that IOD events during the middle Holocene were characterized by a longer duration of strong surface ocean cooling, together with droughts that peaked later than those expected by El Niño forcing alone. Climate model simulations suggest that this enhanced cooling and drying was the result of strong cross-equatorial winds driven by the strengthened Asian monsoon of the middle Holocene. These IOD-monsoon connections imply that the socioeconomic impacts of projected future changes in Asian monsoon strength may extend throughout Australasia.