We report fossil coral records from the Seychelles comprising individual time slices of 14–20 sclerochronological years between 2 and 6.2 kyr BP to reconstruct changes in the seasonal cycle of western Indian Ocean sea surface temperature (SST) compared to the present (1990–2003). These reconstructions allowed us to link changes in the SST bimodality to orbital changes, which were causing a reorganization of the seasonal insolation pattern. Our results reveal the lowest seasonal SST range in the Mid-Holocene (6.2–5.2 kyr BP) and around 2 kyr BP, while the highest range is observed around 4.6 kyr BP and between 1990 and 2003. The season of maximum temperature shifts from austral spring (September to November) to austral autumn (March to May), following changes in seasonal insolation over the past 6 kyr. However, the changes in SST bimodality do not linearly follow the insolation seasonality. For example, the 5.2 and 6.2 kyr BP corals show only subtle SST differences in austral spring and autumn. We use paleoclimate simulations of a fully coupled atmosphere–ocean general circulation model to compare with proxy data for the Mid-Holocene around 6 kyr BP. The model results show that in the Mid-Holocene the austral winter and spring seasons in the western Indian Ocean were warmer while austral summer was cooler. This is qualitatively consistent with the coral data from 6.2 to 5.2 kyr BP, which shows a similar reduction in the seasonal amplitude compared to the present day. However, the pattern of the seasonal SST cycle in the model appears to follow the changes in insolation more directly than indicated by the corals. Our results highlight the importance of ocean–atmosphere interactions for Indian Ocean SST seasonality throughout the Holocene. In order to understand Holocene climate variability in the countries surrounding the Indian Ocean, we need a much more comprehensive analysis of seasonally resolved archives from the tropical Indian Ocean. Insolation data alone only provides an incomplete picture.