Nanohardness (H) and elastic modulus (E) properties of several biomass by-products (fruit shells) have been characterized by nanoindentation technique. Two procedures were followed: (i) 3D topographic images for the microstructure characterization and (ii) 2D mechanical mapping for density and mechanical distribution features analysis. Results revealed the typical cellulosic cell wall structures, indicating that the reduced modulus values (Er) for the cellulosic cells and the amorphous matrix phases were of 6.2 GPa and 4 GPa, respectively, for the apricot shell. The single phases of the rest of structures were tested, showing differences in modulus due to the content of cellulose in the hierarchical structure, and various H and Er features for each specimen and microstructure analyzed.