The geothermal heat flow in the Bellingshausen Sea, West Antarctica, is not well constrained, but a crucial parameter, as it can influence sliding conditions at the ice-bed contact and englacial temperatures and consequently, the ice-sheet flow dynamics. Furthermore, the magnitude and spatial variability of geothermal heat flow can provide insights into regional tectonic and magmatic development. However, bottom water variations of the modified Circumpolar Deep Water are presumably affecting the upper meters of the sub-seafloor sediment temperatures and thus, the measurement-derived heat flow estimates. For these purposes, we conducted heat flow measurements during cruise PS134 in the Bellingshausen Sea at stations located in Ronne Entrance, Eltanin Bay, and in front of the Abbot Ice Shelf. The dataset comprises in situ sediment temperatures measured using a heat flow probe with six Miniaturized Temperature Data-Loggers. Thermal conductivities were measured on split sediment cores using the KD2 Thermal Property Analyzer. During the deployment of the heat flow probe, water column temperatures were recorded.