This article, related to the paper published by Zanola et al. (2024), provides the comprehensive dataset for the first high-resolution δ18O and δ13C records across the Piacenzian – Gelasian boundary (circa 2.6 Ma) in the Gelasian type-area of Monte San Nicola, Sicily (Southern Italy). 230 samples from the lower portion of the "Mandorlo" section of Capraro et al. (2022) were investigated for reconstructing the climate variability of the Central Mediterranean region during the onset of the Northern Hemisphere Glaciation (NHG). Among these, 30 low-resolution samples (sampling pace of 33 cm) were employed for reconstructing a low-resolution record for G. ruber and C. pachyderma, while 200 samples (sampling pace of 5 cm) were handpicked for achieving a high-resolution benthic δ18O and δ13C record for Uvigerina spp. Wavelet power spectrum analysis of the isotopic record highlights a clear signal from components in both the orbital and sub-orbital (millennial) time domains.