This study was conducted to evaluate discrepancies between SST proxies and to assess their sensitivity to oceanographic changes. These data contribute to improved proxy interpretation, particularly for paleoceanographic reconstructions in subtropical ocean settings. This dataset provides sea surface temperature (SST) reconstructions over the past 1.25 million years from sediment core MD96-2048, collected at 660 m water depth near Delagoa Bight in the southwestern Indian Ocean (26°10.482′S, 34°01.148′E) during the Marion Dufresne MD104 cruise. The dataset includes Mg/Ca ratios geochemical records from planktonic foraminifera, presented at low resolutions (10 datapoints). Mg/Ca analyses were conducted on Trilobatus sacculifer (new data presented here), and compared with Mg/Ca on Globigerinoides ruber (published by Caley et al., 2011; doi:10.5194/cp-7-1285-2011) using inductively coupled plasma optical emission spectrometry (ICP-OES). Clumped isotope measurements were performed on G. ruber and are available in the EarthChem dataset. The age model is based on benthic foraminiferal δ¹⁸O stratigraphy from the same core (Caley et al., 2011, doi:10.5194/cp-7-1285-2011). The dataset spans the Quaternary period, with temporal coverage from 0 to 1.25 million years before present. Sampling resolution for Mg/Ca of T. sacculifer is very low (10 datapoints over the last 1.25 Ma), allowing for investigation of differences between Mg/Ca and clumped isotopes.SSTs were primarily calculated using the T. sacculifer Mg/Ca–temperature calibration from Anand et al. (2003, doi:10.1029/2002PA000846), applying the equation with the constant A assumed for this morphotype (with sac). To account for salinity-related biases in Mg/Ca, calibration adjustments based on Gray and Evans (2019, doi:10.1029/2018PA003517) were also incorporated. Data are provided as tabulated time series of raw geochemical measurements and calculated SST estimates.