The Global Stratotype Section and Point for the Palaeocene/Eocene (P/E) boundary was defined at Dababiya Quarry (Egypt) at the base of the carbon isotope excursion (CIE). We present the first detailed analysis of Palaeocene–Eocene benthic foraminifera from Dababiya, in order to infer the palaeoenvironmental turnover across the P/E boundary. At Dababiya, the CIE coincides with a major turnover in foraminiferal assemblages; the last occurrence of Angulogavelinella avnimelechi, at the base of the CIE, may be correlated to the main phase of extinction of deep‐sea benthic foraminifera. Benthic foraminifera indicate that stressful conditions such as oxygen deficiency, carbonate dissolution, and changes in food supply, persisted at the sea floor over most of the CIE interval. The main phase of recovery of benthic foraminifera is recorded c. 250 cm above the P/E boundary, and it may be linked to increased productivity and oxygenation at the sea floor.