This study investigates the effect of the microstructure of electrodeposited ZnNi coatings, in particular pores and microcracks, on hydrogen diffusion characteristics at room temperature. The hydrogen permeation behavior and thermal desorption spectra of electrodeposited ZnNi micro- and nanostructured coatings were studied and compared. The microstructures of the coatings were observed using a scanning electron microscope. The results showed that the presence of microcracks significantly influences the hydrogen diffusion behavior: in microstructured ZnNi hydrogen can diffuse along the microcracks due to the large number of microcracks present, leading to higher hydrogen absorption during electrochemical charging. Also, the high grain boundary density in the nanostructured coating leads to the presence of a larger number of strong H traps, and thus lower diffusible H content.