Three polymetallic nodules from the eastern Clarion-Clipperton Fracture Zone (CCZ), equatorial Pacific Ocean, were analysed to document their internal texture and geochemical composition. Polished thin sections of the three nodules were examined using Scanning Electron Microscopy - Energy Dispersive Spectroscopy (SEM-EDS) to obtain semi-quantitative measurements of major and minor element concentrations along cross-sectional transects. The analyses were conducted at microlayer scale within different growth laminae of the nodules. The dataset was generated to characterize small-scale compositional variability of CCZ polymetallic nodules and to provide quantitative geochemical data for studies on nodule growth structures and formation processes.