Topological defects—extended lattice deformations that are robust against local defects and annealing—have been exploited to engineer novel properties in both hard and soft materials. Yet, their formation kinetics and nanoscale three-dimensional structure are poorly understood, impeding their benefits for nanofabrication. We describe the fabrication of a pair of topological defects in the volume of a single-diamond network (space group Fd3¯m) templated into gold from a triblock terpolymer crystal. Using X-ray nanotomography, we resolve the three-dimensional structure of nearly 70,000 individual single-diamond unit cells with a spatial resolution of 11.2 nm, allowing analysis of the long-range order of the network. The defects observed morphologically resemble the comet and trefoil patterns of equal and opposite half-integer topological charges observed in liquid crystals. Yet our analysis of strain in the network suggests typical hard matter behaviour. Our analysis approach does not require a priori knowledge of the expected positions of the nodes in three-dimensional nanostructured systems, allowing the identification of distorted morphologies and defects in large samples.