Green hydrogen, produced mainly by electrolysis, is a promising energy carrier to de-fossilise different economy sectors, from heavy industry to logistics. A fully transformed economy would use hydrogen as a process gas and a fuel for heat generation and vehicles. However, since the technology to produce green hydrogen has yet to be available at an industrial scale, there are no projections for forming regional hydrogen hubs. This article contributes to synthesising a holistic framework to specify and optimise hydrogen-based applications in logistics from an ecological and economic perspective. These applications utilise logistics macrostructures, like logistics hubs. Alternatively, they may utilise industrial supply chains, like direct reduced iron (DRI) based steel plants, which modify their operations and transform their logistic ecosystems. The framework includes a configuration of policies and economic boundary conditions that influence the logistic hubs’ transformation paths. The article describes the synthesis of the framework based on an initial problem analysis and a systematic literature review. The framework helps policymakers and planners evaluate and optimise the composition and design of hydrogen and logistics hubs.