Changes in the strength of Atlantic meridional overturning circulation (AMOC) are known to have profound impacts on global climate. Coupled modelling studies have suggested that, on annual to multi-decadal time scales, a slowdown of AMOC causes a deepening of the thermocline in the tropical Atlantic. However, this process has been poorly constrained by sedimentary geochemical records. Here, we reconstruct surface (UK'37 Index) and thermocline (TEXH86) water temperatures from the Guinea Plateau Margin (Eastern tropical Atlantic) over the last two glacial–interglacial cycles (~ 192 kyr). These paleotemperature records show that periods of reduced AMOC, as indicated by the d13 C benthic foraminiferal record from the same core, coincide with a reduction in the near-surface vertical temperature gradient, demonstrating for the first time that AMOC-induced tropical Atlantic thermocline adjustment exists on longer, millennial time scales. Modelling results support the interpretation of the geochemical records and show that thermocline adjustment is particularly pronounced in the eastern tropical Atlantic. Thus, variations in AMOC strength appear to be an important driver of the thermocline structure in the tropical Atlantic from annual to multi-millennial time scales.