The effect of microstructure on the efficiency of shielding or shunting of the magnetic flux by permalloy shields was investigated in the present work. For this purpose, the FeNi shielding coatings with different grain structures were obtained using stationary and pulsed electrodeposition. The coatings’ composition, crystal structure, surface microstructure, magnetic domain structure, and shielding efficiency were studied. It has been shown that coatings with 0.2–0.6 µm grains have a disordered domain structure. Consequently, a higher value of the shielding efficiency was achieved, but the working range was too limited. The reason for this is probably the hindered movement of the domain boundaries. Samples with nanosized grains have an ordered two-domain magnetic structure with a permissible partial transition to a superparamagnetic state in regions with a grain size of less than 100 nm. The ordered magnetic structure, the small size of the domain, and the coexistence of ferromagnetic and superparamagnetic regions, although they reduce the maximum value of the shielding efficiency, significantly expand the working range in the nanostructured permalloy shielding coatings. As a result, a dependence between the grain and domain structure and the efficiency of magnetostatic shielding was found.