We present a combined phase field and cohesive zone formulation for hydrogen embrittlement that resolves the polycrystalline microstructure of metals. Unlike previous studies, our deformation-diffusion-fracture modelling framework accounts for hydrogen-microstructure interactions and explicitly captures the interplay between bulk (transgranular) fracture and intergranular fracture, with the latter being facilitated by hydrogen through mechanisms such as grain boundary decohesion. We demonstrate the potential of the theoretical and computational formulation presented by simulating inter- and trans-granular cracking in relevant case studies. Firstly, verification calculations are conducted to show how the framework predicts the expected qualitative trends. Secondly, the model is used to simulate recent experiments on pure Ni and a Ni–Cu superalloy that have attracted particular interest. We show that the model is able to provide a good quantitative agreement with testing data and yields a mechanistic rationale for the experimental observations.