This data set reports two highly resolved δ¹¹B-derived CO₂ records during the late Pleistocene (0-400 ky) from ODP Sites 999 (Caribbean) and 871 (West Pacific) based on the δ¹¹B of the planktonic foraminifera species Globigerinoides ruber measured by MC-ICPMS (multicollector inductively coupled plasma mass spectrometer). The δ¹¹B-derived CO₂ is tested against the ice core CO₂ record as well as compared with different CO₂ calculation approaches and proxies of local foraminifera dissolution to evaluate drivers of CO₂ offset between the two records. We report (1) δ¹¹B, Mg/Ca and input data for boron-derived CO₂ calculation, (2) Mg/Ca-derived sea surface temperature calculated with various approaches, (3) the effect of Mg/Ca treatment on boron-derived CO₂, (4) δ¹⁸O and δ¹³C of benthic foraminifera and G. ruber, and (5) fragmentation index and sand fraction.