This dataset contains Mg/Ca, Sr/Ca and Mn/Ca data from IODP Site U1488 in the central Western Pacific Warm Pool measured in two species of planktonic foraminifera, Trilobatus trilobus and Globorotalia tumida. The trace element data was generated at the University of California, Santa Cruz (UCSC) using a Thermo Fisher iCAP 7400 ICP-OES. The dataset also contains water temperature reconstructions for both species based on the Mg/Ca data applying various corrections and using published Mg/Ca to temperature calibrations. The data covers eight time intervals from the last 5.6 Myrs. Trace element and Mg/Ca-based temperature data are presented for each sample within these time intervals. Additionally, for each of the time intervals average calcification temperatures based on clumped isotope data and Mg/Ca ratios were calculated. Clumped isotope measurements were performed at the University of Bergen, Norway, using a Thermo Scientific MAT 253Plus mass spectrometer coupled to a KIEL IV carbonate device.