The thermal state of the lithosphere and related geothermal heat flow (GHF) is a crucial parameter to understand a variety of processes related to cryospheric, geospheric, and/or biospheric interactions. Indirect estimates of GHF in polar regions from magnetic, seismological, or petrological data often show large discrepancies when compared to thermal in situ observations. Here, the lack of in situ data represents a fundamental limitation for both investigating thermal processes of the lithosphere and validating indirect heat flow estimates. During RV Polarstern expeditions PS86 and PS118, we obtained in situ thermal measurements and present the derived GHF in key regions, such as the Antarctic Peninsula and the Gakkel Ridge in the Arctic. By comparison with indirect models, our results indicate (1) elevated geothermal heat flow (75 ± 5 mW m−2 to 139 ± 26 mW m−2 ) to the west of the Antarctic Peninsula, which should be considered for future investigations of ice-sheet dynamics and the visco-elastic behavior of the crust. (2) The thermal signature of the Powell Basin characteristic for oceanic crust of an age between 32 and 18 Ma. Further, we propose (3) that at different heat sources at the slow-spreading Gakkel Ridge in the Aurora Vent Field region might explain the geothermal heat flow distribution. We conclude that in situ observations are urgently required to ground-truth and fine-tune existing models and that a multidisciplinary approach is of high importance for the scientific community’s understanding of this parameter.