The early Eocene (56–48 Ma) hothouse experienced the highest CO2 levels of the Cenozoic, as well as the occurrence of multiple transient global warming events, so-called hyperthermals. The deep ocean constitutes a stable and vast heat reservoir in the climate system, and hence compromises a robust setting to estimate past global mean temperatures. However, available deep-sea temperature reconstructions rely on uncertain assumptions of non-thermal influences. Here, we apply for the first time the carbonate clumped isotope paleothermometer (Δ47), a proxy not governed by these uncertainties, on early Eocene benthic foraminifera to evaluate South Atlantic deep-sea temperatures across two hyperthermal events (ETM2 and H2; ~54 Ma). In comparison to the conventional δ18O-based estimates, our new temperature reconstructions indicate two and a half degrees warmer deep water conditions, i.e. 13.2±1.9 °C (95% Confidence Interval) for background state, and average deep-sea warming of 3.3±2.9 °C (95% CI) during these hyperthermal events. These findings imply a reassessment of the assumed isotope composition of the ancient seawater and of a potential pH effect on foraminiferal oxygen isotopes. On a broad scale, our Δ47-based overall warmer deep-sea temperatures provide new evidence for high climate sensitivity during the early Eocene hothouse.