The geochemical and mineralogical characteristics of pelagic sediments collected from the Interoceanmetal Joint Organization (IOM) claim area, located in the eastern part of the Clarion-Clipperton Fracture Zone (CCFZ; eastern tropical Pacific), are described in this paper. The concentrations of rare earth elements (REE), as well as other selected critical elements contained in 135 sediment samples of siliceous clayey silts, are presented. The vertical and spatial variabilities of elements, with particular emphasis on REE as well as metals of the highest economic interest such as Cu, Ni, and Co, are detailed. The applied methods include grain size analysis by laser diffraction, geochemistry examination using ICP-MS, XRF, AAS, and CNS spectrometry, and XRD analysis of mineral composition (Rietveld method). Additionally, statistical methods such as factor analysis (FA) and principal components analysis (PCA) were applied to the results. Finally, a series of maps was prepared by geostatistical methods (universal kriging). Grain size analysis showed poor sorting of the examined fine-grained silts. ICP-MS indicated that total REE contents varied from 200 to 577 ppm, with a mean of 285 ppm, which is generally low. The contents of critical metals such as Cu, Ni, and Co were also low to moderate, apart from some individual sampling stations where total contents were 0.15% or more. Metal composition in sediments was dominated by Cu, Ni, and Zn. A mineral composition analysis revealed the dominance of amorphous biogenic opaline silica (27–58%), which were mostly remnants of diatoms, radiolarians, and sponges associated with clay minerals (23% to 48%), mostly Fe-smectite and illite, with mixed-layered illite/smectite. The high abundance of diagenetic barite crystals found in SEM−EDX observations explains the high content of Ba (up to 2.4%). The sediments showed complex lateral and horizontal fractionation trends for REE and critical metals, caused mostly by clay components, early diagenetic processes, admixtures of allogenic detrital minerals, or scavenging by micronodules.