The bioactivity, biological fate and cytotoxicity of nanomaterials when they come into contact with living organisms are determined by their interaction with biomacromolecules and biological barriers. In this context, the role of symmetry/shape anisotropy of both the nanomaterials and biological interfaces in their mutual interaction, is a relatively unaddressed issue. Here, we study the interaction of gold nanoparticles (NPs) of different shapes (nanospheres and nanorods) with biomimetic membranes of different morphology, i.e. flat membranes (2D symmetry, representative of the most common plasma membrane geometry), and cubic membranes (3D symmetry, representative of non-lamellar membranes, found in Nature under certain biological conditions). For this purpose we used an ensemble of complementary structural techniques, including Neutron Reflectometry, Grazing Incidence Small-Angle Neutron Scattering, on a nanometer lengthscale and Confocal Laser Scanning Microscopy on a micrometer length scale. We found that the structural stability of the membrane towards NPs is dependent on the topological characteristic of the lipid assembly and of the NPs, where a higher symmetry gave higher stability. In addition, Confocal Laser Scanning Microscopy analyses highlighted that NPs interact with cubic and lamellar phases according to two distinct mechanisms, related to the different structures of the lipid assemblies. This study for the first time systematically addresses the role of NPs shape in the interaction with lipid assemblies with different symmetry. The results will contribute to improve the fundamental knowledge on lipid interfaces and will provide new insights on the biological function of phase transitions as a response strategy to the exposure of NPs.