AbstractSomali upwelling is the fifth largest upwelling globally with high productivity, attracting tuna migratory species. A key control on the upwelling productivity is its interaction with one of the world’s largest oceanic eddies, the Great Whirl inducing a strong downwelling signal. Here, we use satellite-derived observations to determine the Great Whirl impact on the extent of the upwelling-driven phytoplankton bloom. We find that following decreases in upwelling intensity, productivity has declined by about 10% over the past two decades. The bloom extent has also been diminishing with an abrupt decrease around 2006–2007, coinciding with an abrupt increase in the downwelling effect. Absent or weak Great Whirl leads to the occurrence of smaller anticyclonic eddies with a resulting downwelling stronger than when the Great Whirl is present. We suggest that 2006–2007 abrupt changes in the bloom and downwelling extents’ regimes, are likely driven by Indian Ocean Dipole abrupt shift in 2006.