Alkenones and Glycerol Dialkyl Glycerol Tetraether lipids (GDGT) as remnants of living organisms are widely used biomarkers for determining past oceans’ water temperatures. The organisms these proxy carriers stem from, are influenced by a number of environmental parameters, such as water depth, nutrient availability, light conditions or seasonality, which all may significantly bias the calibration to ambient water temperatures. Reliable temperature determinations remain thus challenging, especially in higher latitudes and for under-sampled regions. We analyzed 33 sediment surface samples from the Southern Chilean continental margin and the Drake Passage for alkenones and GDGTs and compared the results with gridded instrumental reference data from the World Ocean Atlas 2005 (WOA05), as well as previously published data from an extended study area covering the Central and Western South Pacific towards the New Zealand continental margin. We show that for alkenone-derived SSTs, the widely-used global core-top calibration of Müller et al. (1998) yields the smallest residuals, whereas the calibration of Sikes et al. (1997), adapted to higher latitudes and supposed to show summer SSTs, overestimates modern WOA05-based (summer and annual mean) SSTs. Our alkenone SSTs show a slight seasonal shift of ~1 °C at the Southern Chilean Margin and up to ~2 °C in the Drake Passage towards austral summer SSTs, whereas samples in the Central South Pacific reflect an annual mean signal. We show that for GDGT-based temperatures, a more complex pattern emerges. In areas north of the Subantarctic Front (SAF) the subsurface calibration of Kim et al. (2012a) best reflects temperatures from the WOA05, largely within the margin error of ±2.2 °C. Temperatures south of the SAF instead are significantly overestimated by up to 14 °C, irrespective of the applied calibration. Based on a qualitative assessment of the GDGT [2] / [3]-ratios, which likely indicate water depth of origin, our samples reflect a subsurface (0 to 200 m water depth) rather than a surface (0–50 m water depth) signal. The overestimation of surface and subsurface temperatures south of the SAF highlights the need for a re-assessment of existing calibrations in the polar Southern Ocean, and leads to limitations in reliably both obtaining absolute values and assessing relative changes. Therefore, we suggest a modified Southern Ocean calibration for surface and subsurface GDGT-based temperatures, which shows a lower temperature sensitivity of the TEXL86 and yields principally lower absolute temperatures, which align more closely with WOA05-derived values.