Abstract We studied two boreholes (Cserepvaralja-1 and Kiscell-1) with continuous sedimentary records across the Eocene-Oligocene climate transition from the Central Paratethyan area. Assemblages of benthic foraminifera display a shift in dominance by epifaunal taxa in the late Eocene to shallow and deep infaunal taxa in the early Oligocene. Using the benthic foraminiferal oxygen index (BFOI), a decreasing trend of bottom-water oxygen levels is established across the Eocene-Oligocene transition (EOT), leading to the development of dysoxic conditions later in the early Oligocene. Trends in δ18O and δ13C values measured on tests of selected benthic and planktic foraminifera roughly parallel those of the global record of stepped EOT δ18O increase and deviate only later in the early Oligocene, related to the isolation of the Paratethys. The overall similarity of the isotope curves and the presence of a planktic-benthic ecological offset suggest that the original isotope trends are preserved, despite the systematically more negative δ18O values. Of different scenarios, a quasi-uniform diagenetic overprint by fluids with low δ18O values, during burial or uplift, appears best supported. We conclude that the globally established isotopic expression of Antarctic ice sheet growth across the EOT may be recognizable in the Paratethys. Deviations from the global trends after the EOT were caused by regional paleoceanographic changes induced by the progressing Alpine orogeny and sea-level change, which led to a restricted connection with the open ocean, freshwater influx from increased precipitation, and gradual development of bottom-water oxygen depletion.