The scope of this paper is the development and implementation of a safety risk assessment methodology to highlight hazards potentially prevailing during autothermal reforming of natural gas for hydrogen production in a membrane reactor, as well as to reveal potential accidents related to hydrogen under certain conditions. The newly developed methodology is able to cover all possible risk scenarios. The methodology was applied to a novel autothermal membrane fluidized bed reactor integrated within a micro-CHP system of 5 kWel with a PEM fuel cell. The system modelled is based on a prototype developed within the European ReforCELL project. A thorough safety risk assessment methodology was applied examining and evaluating the final outcomes of hydrogen release accident scenarios. The main conclusion of this analysis is that hydrogen may lead to a series of accident types that may pose a threat to the public safety, however, all considered scenarios fall well within the standard criteria, which indicates the adequate safety of this novel technology.