Coconut kernel shell (CKS) and palm kernel shell (PKS) powders were analyzed using Surface Electron Microcopy (SEM) and Transmission Electron Microscopy (TEM). The SEM and TEM were combined with Energy Dispersive X-ray Spectroscopy Analysis for elemental composition of the sample materials. The micrographs of all samples were thoroughly examined and explained. The dataset presented herein helps to elucidate the ultrastructure and could suggest expanding traditional applications of the PKS/CKS to novel ones. The data are related to the research article “Insight on the Ultrastructure, Physicochemical and Thermal Characteristics and Applications of the Palm Kernel Shells” (Ntenga et al., 2018). Keywords: Palm kernel shell, Coconut kernel shell, SEM and TEM, EDS and EDXA