TEX₈₆ is a paleothermometer based on Thaumarcheotal glycerol dialkyl glycerol tetraether (GDGT) lipids and is one of the most frequently used proxies for sea-surface temperature (SST) in warmer-than-present climates. However, GDGTs are not exclusively produced in and exported from the mixed layer, so sedimentary GDGTs may contain a depth-integrated signal that is also sensitive to local subsurface temperature variability. In addition, the correlation between TEX₈₆ and SST is not significantly stronger than that to depth-integrated mixed-layer to subsurface temperatures. The calibration of TEX₈₆ to SST is therefore controversial. Here we assess the influence of subsurface temperature variability on TEX₈₆ using a downcore approach. We present a 15 Myr TEX₈₆ record from Ocean Drilling Program Site 959 in the Gulf of Guinea and use additional proxies to elucidate the source of the recorded TEX₈₆ variability. Relatively high GDGT ratio values from 13.6 Ma indicate that sedimentary GDGTs were partlysourced from deeper (>200 m) waters. Moreover, late Pliocene TEX ₈₆ variability is highly sensitive to glacial–interglacial cyclicity, as is also recorded by benthic δ¹⁸O, while the variability within dinoflagellate assemblages and surface/thermocline temperature records (U and ) is not primarily explained by glacial–interglacial cyclicity. Combined, these observations are best explained by TEX₈₆ sensitivity to sub-thermocline temperature variability. We conclude that TEX₈₆ represents a depth-integrated signal that incorporates a SST and a deeper component, which is compatible with the present-day depth distribution of Thaumarchaeota and with the GDGT distribution in core tops. The depth-integrated TEX₈₆ record can potentially be used to infer SST variability, because subsurface temperature variability is generally tightly linked to SST variability. Using a subsurface calibration with peak calibration weight between 100 and 350 m, we estimate that east equatorial Atlantic SST cooled by ∼5 ^∘C between the Late Miocene and Pleistocene. On shorter timescales, we use the TEX₈₆ record as a proxy for South Atlantic Central Water (SACW), which originates from surface waters in the South Atlantic Gyre and mixes at depth with Antarctic Intermediate Water (AAIW). Leads and lags around the Pliocene M2 glacial (∼3.3 Ma) in our record, combined with published information, suggest that the M2 glacial was marked by SACW cooling during an austral summer insolation minimum and that decreasing CO₂ levels were a feedback, not the initiator, of glacial expansion.