<p>TEX<sub>86</sub> 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, the calibration of TEX<sub>86</sub> to SST is controversial because its correlation to SST is not significantly stronger than that to depth-integrated surface to subsurface temperatures. Because GDGTs are not exclusively produced in and exported from the surface ocean, sedimentary GDGTs may contain a depth-integrated signal that is sensitive to local subsurface temperature variability, which can only be proved in downcore studies. Here, we present a 15 Myr TEX<sub>86</sub> record from ODP Site 959 in the Gulf of Guinea and use additional proxies to elucidate the source of the recorded TEX<sub>86</sub> variability. Relatively high GDGT[2/3] ratio values from 13.6 Ma indicate that sedimentary GDGTs were partly sourced from deeper (> 200 m) waters. Moreover, late Pliocene TEX<sub>86</sub> variability is highly sensitive to glacial-interglacial cyclicity, as is also recorded by benthic δ<sup>18</sup>O, while the variability within dinoflagellate assemblages and surface/thermocline temperature records (U<sup>k’</sup>37 and Mg/Ca), is not primarily explained by glacial-interglacial cyclicity. Combined, these observations are best explained by TEX<sub>86</sub> sensitivity to sub-thermocline temperature variability. We conclude that the TEX<sub>86</sub> record represents a depth-integrated signal that incorporates a SST and a deeper component, which is compatible the present-day depth distribution of Thaumarchaeota and with the GDGT[2/3] distribution in core tops. The depth-integrated TEX<sub>86</sub> 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 100–350 m, we estimate that east equatorial Atlantic SST cooled by ~4.5 °C between the Late Miocene and Pleistocene. On shorter timescales, we use the TEX<sub>86</sub> record as an Antarctic Intermediate Water (AAIW) proxy and evaluate climatological leads and lags around the Pliocene M2 glacial (~3.3 Ma). Our record, combined with published information, suggests that the M2 glacial was marked by AAIW cooling during an austral summer insolation minimum, and that decreasing CO<sub>2</sub> levels were a feedback, not the initiator, of glacial expansion.</p>