Sediment cores were collected using a piston corer at three sites in the eastern Mediterranean Sea. Piston cores MS21 (32°20.7'N, 31°39.0'E; 1022 m water depth; 751.5 cm in length) and MS66 (33°1.9'N, 31°47.9'E; 1630 m water depth; 630 cm in length) were recovered during the MIMES cruise with the R/V Pelagia in 2004. Piston core 64PE406E1 (33°18.1'N, 33°23.7'E; 1760 m water depth; 920.5 cm in length) was recovered during the Eastern Mediterranean part of the 64PE406 (NESSC) cruise with the R/V Pelagia in 2016. The cores were opened and then prepared for X-Ray Fluorescence (XRF) core scanning by carefully flattening the sediment and covering it with a 4-μm SPEXCerti Ultralene foil. Subsequently, the sediments were XRF-scanned with a 1-mm resolution using four settings (10 kV-no filter, 20 kV-Al filter, 30 kV-Pd-thick filter, and 50 kV-Cu filter). The produced XRF-core-scanner data were calibrated using a subset of the discrete samples taken from the same core material. These samples were digested with an acid mixture and partially measured by inductively coupled plasma mass spectrometry (ICP-MS) and partially measured by ICP-optical emission spectroscopy (ICP-OES). The main purpose of our data collection was to reconstruct in detail (~10-50 yr resolution) the deoxygenation and anoxia in the eastern Mediterranean Sea during the last 300 ka BP; we focused on elements and elemental ratios of Al, Ba, Mo, Ti, and U.