This data collection of the ~17 m long piston core MR16-09 PC03 contains age pointers for an age model, major element data (Ti, Rb) from an XRF scan, biomarkers (n-alkanes, alkenones and brGDGTs), and d18O from foraminifera (G. bulloides and G. truncatulinoides). The piston core MR16-09 PC03 is located near the southern Chilean continental margin, at a distance of ~150 km. In addition, there are alkenone data (C37:4) from sites GeoB3327 and PS75/034 (Ho et al., 2012), which are located north and south of MR16-09 PC03, respectively, and further away from the Chilean margin.