The early Eocene hothouse experienced highly elevated atmospheric CO2 levels and multiple transient global warming events, so-called hyperthermals. The deep ocean constitutes an assumed setting to estimate past global mean temperatures. However, available deep-sea temperature reconstructions from conventional benthic foraminiferal oxygen isotopes and magnesium/calcium ratios rely on uncertain assumptions of non-thermal influences, associated with seawater chemistry and species-specific physiological effects. Here we apply the carbonate clumped isotope thermometer, a proxy not governed by these uncertainties, to evaluate South Atlantic deep-sea temperatures across two hyperthermal events in the early Eocene (Eocene Thermal Maximum 2/H1 and H2; ~54 Myr ago). Our independent reconstructions indicate deep-sea temperatures of 13.5 ± 1.9 °C (95% CI) for the background conditions and average hyperthermal peak temperatures of 16.9 ± 2.3 °C (95% CI). On average, these absolute temperatures are three degrees warmer than estimates from benthic oxygen isotopes. This finding implies a necessary reassessment of (1) the Eocene seawater isotope composition and (2) pH changes in the deep ocean and its potential influence on benthic foraminiferal oxygen isotope records.