A 115-year coral record from Kenya has been found to preserve the history of rainfall anomalies in East Africa in relation to global warming-induced Indian Ocean Dipole (IOD) variability. The coral IOD index demonstrates a dominantly decadal periodicity in the early part of the 20th century. This low-frequency IOD occurred more frequently before 1924 with mostly quasi-biennial ranging from 18 months to 3 years events since 1960. The mode shift has also coincided with an intensified coupling with Indian summer monsoon rainfall. We suggest that a warming of the western Indian Ocean, which has attenuated and replaced the El Niño/Southern Oscillation effect over the Indian Ocean, has driven the observed shift.