This dataset provides microfacies data from the sediment profile at Masada (MAS), located at the southwestern shore of the Dead Sea for the last glacial-interglacial transition (ca. 17-11.5 ka BP). The uppermost ~3.8 m sediments of the Lisan Formation were analyzed, which form the terminal deposit at this site. About 1.37 m from the uppermost UGU to the lowermost AGU were sampled continuously for thin section analyses, while macroscopic information is provided for most of the gypsum units. Sampling was performed in 2018 and followed the subsequent procedure: after smoothing the outcrop surface with a sharp knife, stainless steel boxes (~34 cm x 5 cm) with removable side walls were pressed into the sediment along a vertical profile. The boxes were overlapping by several centimeters and a battery-operated dovetail saw was used to cut the hard gypsum sections. At the GFZ in Potsdam, the sediments were carefully transferred into aluminum boxes and impregnated with epoxy resin. Thin sections (10x2 cm) with 2 cm overlap were prepared subsequently. Thin section analyses were performed using a Zeiss Axiolab pol microscope at magnifications of 50-400x. A floating varve chronology was established between the UGU and AGU and anchored at the bottom of the AGU using the transferred age from the new OxCal age model from the ICDP core. Uncertainties are derived from the age model and varve counting. Microfacies analyses included varve counting and measurements of varve and sublayer thickness.