The warm and relatively stable Holocene climate was preceded by a pronounced event of abrupt warming in the Northern Hemisphere, the termination of the Younger Dryas cold period1,2. While this transition has been intensively studied, its imprint on low latitude ocean temperature is still controversial and its effects on sub-annual to decadal climate variability remain poorly understood1,3,4. We applied the extraordinary resolution provided by mass spectrometry imaging of long-chain alkenones5,6 to sediments from the tropical Cariaco Basin7, and reveal that the seasonal amplitude of reconstructed sea surface temperature increased more than twofold during the transition into the Holocene, while average temperature was not altered. We further observe modulations in interannual sea surface temperature variability that we attribute to a muting of the El Niño-Southern Oscillation at the end of the Younger Dryas, and a subsequent intensification during the early Holocene. These dynamics are consistent with the modeled interplay of meltwater and ice sheet forcing and suggest that climate recovery in the Pacific preceded the North Atlantic Younger Dryas-Holocene transition. Our results demonstrate that the abrupt changes that completed the most recent glacial to interglacial transition had pronounced effects on sub-and interannual climate variability in the Tropical North Atlantic.