The evolution of the mixed layer temperature anomalies in the Mozambique Channel is analysed using a mixed layer heat budget covering sub-seasonal to interannual time scales. Sub-seasonal variations in mixed layer temperature are largely dominated by surface heat fluxes, except along the southern coast of Mozambique and Madagascar, where both the advection and the residual terms become significant. The northern Channel is dominated by the mean flow while the southern Channel is modulated by both the mean and eddy terms. Minimum heat gain through advection is observed in the channel during January–February when the Northeast Madagascar current opposes the northwesterly monsoonal winds. During the 1997/98 El Niño/positive Indian Ocean dipole, extreme warming and coral bleaching events were noted in the northern Channel. Such warming was linked with the relaxation of local winds, positive heat gain from the atmosphere and the shedding of large anticyclonic eddies northwest of Madagascar, associated with the arrival of downwelling Rossby waves. By contrast, upwelling Rossby waves and large cyclonic eddies in the Channel occurred during the 1998–2001 protracted La Niña, but only the northern part of the Channel experienced significant negative anomalies in mixed layer temperature. While no coral bleaching hotspots were noted in the northern Channel in summer 1999/2000 due to negative anomalies in advection, marine heatwaves occurred in the southern Channel during that summer. Finally, the protracted 1998–2001 La Niña was the last time that substantial upwelling Rossby wave activity occurred in the tropical South Indian Ocean; recent La Niña events showed muted or weak upwelling Rossby wave activity, including the recent 2020–2022 protracted event. Post-2001 also occurs at the same time as a stronger warming trend in the southwest Indian Ocean region.