Hydrogen embrittlement (HE) causes sudden, costly failures of metal components across a wide range of industries. Yet, despite over a century of research, the physical mechanisms of HE are too poorly understood to predict HE-induced failures with confidence. We use non-destructive, synchrotron-based techniques to investigate the relationship between the crystallographic character of grain boundaries and their susceptibility to hydrogen-assisted fracture in a nickel superalloy. Our data lead us to identify a class of grain boundaries with striking resistance to hydrogen-assisted crack propagation: boundaries with low-index planes (BLIPs). BLIPs are boundaries where at least one of the neighboring grains has a low Miller index facet—{001}, {011}, or {111}—along the grain boundary plane. These boundaries deflect propagating cracks, toughening the material and improving its HE resistance. Our finding paves the way to improved predictions of HE based on the density and distribution of BLIPs in metal microstructures.