The detailed mineralogical and microgeochemical characteristics of polymetallic nodules collected from the Interoceanmetal Joint Organization (IOM, Szczecin, Poland) claim area, Eastern Clarion-Clipperton Fracture Zone (CCFZ, Eastern Pacific) were described in this study. The obtained data were applied for the delimitation of nodule growth generations and estimation of the growth ratios (back-stripping using the Co-chronometer method). The applied methods included bulk X-ray powder diffraction (XRD) and electron probe microanalysis (EPMA), providing information about Mn-Fe minerals and clays composing nodules, as well as the geochemical zonation of the growth generations. The analyzed nodules were mostly diagenetic (Mn/Fe > 5), with less influence on the hydrogenous processes, dominated by the presence of 10-Å phyllomanganates represented by todorokite/buserite, additionally mixed with birnessite and vernadite. The specific lithotype (intranodulith), being an integral part of polymetallic nodules, developed as a result of the secondary diagenetic processes of lithification and the cementation of Fe-rich clays (potentially nontronite and Fe-rich smectite), barite, zeolites (Na-phillipsite), bioapatite, biogenic remnants, and detrital material, occurs in holes, microcaverns, and open fractures in between ore colloforms. The contents of ∑(Ni, Cu, and Co) varied from 1.54 to 3.06 wt %. Several remnants of siliceous microorganisms (radiolarians and diatoms) were found to form pseudomorphs. The applied Co-chronometer method indicated that the nodules’ age is mainly Middle Pliocene to Middle Pleistocene, and the growth rates are typical of diagenetic and mixed hydrogenetic–diagenetic (HD) processes. Additionally, few nodules showed suboxic conditions of nucleation. Growth processes in the eastern part of the CCFZ deposit might have been induced with the Plio-Pleistocene changes in the paleooceanographic conditions related to the deglaciation of the Northern Hemisphere.