This dataset contains carbonate clumped isotope data of the shells of A. benedeni benedeni specimens SG-126 and SG-127 as well as used standards (ETH1, ETH2, ETH3, Merck, IAEA-C2). These measurements were carried out in order to reconstruct a palaeo mean annual temperature from these shells, using the temperature calibration of Meinicke et al. (2020, 2021). The bivalve shells were collected in 2013 from a shell bed at the top of the Oorderen Member of the Lillo Formation of the Pliocene in Belgium. The collection site was a construction-related temporary outcrop at the Deurganck Dock Lock (now Kieldrecht Lock) in the city of Antwerp, located at 51°16′44″N 4°14′52″E. Clumped isotopes were measured in spring 2021 at the department of Earth Sciences at Utrecht University, the Netherlands, on a Kiel IV carbonate device coupled to a Thermo Scientific MAT 253 Plus isotope ratio mass spectrometer and using a LIDI workflow, following the protocol of Meckler et al. (2014). The dataset includes raw data and corrected values, and final values are reported in accordance with the I-CDES90 reference frame of Bernasconi et al. (2021). Associated oxygen and carbon isotopes are reported relative to the Vienna Pee-Dee Belemnite (VPDB) standard.