However, existing van der Waals-based vertical Josephson junctions largely rely on transfer-based assembly schemes that are incompatible with elemental materials such as niobium (Nb). Here, we introduce a freestanding van der Waals membrane architecture that enables deposition-based fabrication of vertical Josephson junctions through double-sided processing of a single suspended two-dimensional layer. Using multilayer graphene suspended across lithographically defined through-holes in a SiNx membrane, we realize vertical Nb/multilayer graphene/Nb Josephson junctions without ambient exposure of buried interfaces. The resulting devices exhibit clear Josephson coupling, including reproducible supercurrents and a temperature dependence of the critical current consistent with short-junction behaviour. Well-defined magnetic interference patterns governed by the membrane-defined aperture geometry, together with sub-gap features that track a Bardeen-Cooper-Schrieffer (BCS)-like superconducting gap, further confirm the junction quality. This platform establishes a scalable route to vertical superconducting devices based on oxidation-sensitive elemental superconductors and van der Waals materials.