This dataset contains the contents of 58 elements and grain-size distribution in 48 sediment samples from sediment cores from six sites with the water depths greater 7.5 km in the Japan Trench. Five of the sediment cores were collected by a giant piston corer up to 40 m long and one by a trigger corer onboard R/V Kaimei during the International Ocean Discovery Program (IODP) expedition 386 Japan Trench Paleoseismology between 13 April and 1 June 2021. The coring sites M0081 and M0082 were located in the Southern Japan Trench expanded and condensed sections, respectively. The sites M0083 and M0089 were located in the Central Japan Trench expanded and condensed sections, respectively. The sites M0084 and M0085 were located in the Northern Japan Trench expanded and condensed sections, respectively. Sediment samples were freeze-dried, homogenized and halved, with one half analysed for multielement composition and the other half for grain size distribution at the laboratory (Eurofins Environment Testing Finland, Jyväskylä; Eurofins Ahma, Oulu). The material for multielement analysis was sieved through a 63 μm mesh, and 0.2 g of the passed-through fraction was digested in a four-acid mixture of hydrofluoric acid, perchloric acid, hydrochloric acid and nitric acid (USGS Methods T01 and T20). After evaporation of the acids at 160 °C, the resulting gel was dissolved to 1 M nitric acid and analysed for element concentrations by inductively coupled plasma-mass spectrometry (ICP-MS), or inductively coupled plasma-optical emission spectrometry (ICP-OES). Al, B, Ba, Ca, Cr, Cu, Fe, K, Mg, Mn, Na, Ni, P, S, Sr, Ti, V, and Zn were analysed by ICP-OES, whereas Ag, As, Be, Bi, Cd, Ce, Co, Dy, Er, Eu, Gd, Hf, Ho, La, Li, Lu, Mo, Nb, Nd, Pb, Pr, Rb, Sb, Sc, Sm, Sn, Ta, Tb, Te, Th, Tl, Tm, U, W, Y, Yb, and Zr were analysed by ICP-MS. Commercial sediment reference materials and in-house standards were used for assessing measurement accuracy. Element concentrations for all reference materials measured with each sample batch fell well within ±10 % of the certified values. Mercury was measured separately for 0.2 g samples through thermal decomposition, amalgamation and atomic absorption spectrometry (US EPA Method 7473). Solid-phase contents of C and N in the samples were analyzed by high-temperature combustion elemental analysis (ISO 16948 method). The material for grain size distribution analysis was treated with excess hydrogen peroxide to remove organic matter. No sieving was performed because of the fine grain size of the samples. Sediment grain size distribution was determined down to 0.6 μm using a Micromeritics Sedigraph III 5120 X-ray absorption sedimentation analyzer. The values in the depth column refer to the depth of the center of the 2-cm-thick samples. The full sample interval is depth +/- 1 cm.