This data set is part of a larger data harmonization effort to make lake sediment core data machine readable and comparable. Here we standardized X-ray fluorescence line scanning (XRF)-based element data of sediment core PG2360, retrieved in 2016 from Lake Bety (Yakutia, Russia) at 1.5 m water depth. The thermokarst lake Bety is a small thermkarst lake in the coniferous forest area and has one outflow and three inflows. It lies at an elevation of ca. 160 m a.s.l. with a surface area of ca. 0.66 km2 and a maximum lake water depth of estimated 1.5 m. The 2.31 m sediment core was retrieved by a Russian peat corer during the Expedition Yakutia 2016 of the Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research (AWI, Germany, Potsdam) in cooperation with the North Eastern Federal State University (NEFU, Russia, Yakutsk). The downcore elemental composition was measured using an AVAATECH x-ray fluorescence core scanner at AWI Bremerhaven.