The data set compiles gamma-ray wet bulk density, magnetic susceptibility (MS), and XRF core scans of the three cores GeoB16433-1 (38° 07.843'N, 144° 00.135'E, 7,525 m water depth), GeoB16431-1 (38° 00.177'N, 143° 59.981'E, 7,542 m water depth), and GeoB16444-1 (37° 42.017'N, 143° 52.377'E, 7,529 m water depth) retrieved from the central Japan Trench during Sonne Cruise SO219A in 2012. Gamma-ray wet bulk density and MS were measured by using the Geotek multi-sensor core logger at MARUM, University of Bremen. XRF core scans (elements: Al, Si, S, K, Ca, Ti, Mn, Fe, Br, Rb, Sr, Zr) were analyzed by using the Avaatech XRF core scanner at MARUM, University of Bremen.