Lamellar structures self-assembled from purple membranes (PM) of Halobacterium salinarum are promising building units for bio-electronic devices, due to proton pumping ability of the PM. The functionality and durability of such devices are hinged on the structural integrity of PM lamellae. Using X-ray diffraction, we examined the structure of PM multilayers on silicon when challenged with two types of nanoparticles (NPs): carboxymethyl-dextran coated magnetite (2.4 nm core size) and citrate-stabilised gold (5 nm core size). We tried to infiltrate the PM multilayers with the NPs using two alternative routes: facile penetration (FP) and co-assembly (CS) by solution mixing. We found that under all conditions the NPs did not disrupt the overall lamellar structure of the PM films or enter the inter-lamellar space, although the presence of NPs affected the self-assembly process of the PM films. This caused an increase in the disorder in the film structure, as assessed by the decreasing number of layers in the multilayer stack as the NP concentration increased. Despite this, UV-Vis spectroscopic measurements showed that the conformation of the retinal residue within the protein was intact so the proton pumping functionality of PM multilayers would be retained in all samples with added NPs. Our results show that the effects of NPs on the PM structure and functionality are subtle and complex, and we will discuss the structural integrity of lipid-protein composite PM films against NP infiltration in terms of their high bending modulus as compared with that of fluid lipid bilayers.