Hydrogen derived from biomass feedstock (biohydrogen) can play a significant role in Germany’s hydrogen economy. However, the bioenergy potential and environmental benefits of biohydrogen production are still largely unknown. Additionally, there are no uniform evaluation methods present for these emerging technologies. Therefore, this paper presents a methodological approach for the evaluation of bioenergy potentials and the attainable environmental impacts of these processes in terms of their carbon footprints. A procedure for determining bioenergy potentials is presented, which provides information on the amount of usable energy after conversion when applied. Therefore, it elaborates a four-step methodical conduct, dealing with available waste materials, uncertainties of early-stage processes, and calculation aspects. The bioenergy to be generated can result in carbon emission savings by substituting fossil energy carriers as well as in negative emissions by applying biohydrogen production with carbon capture and storage (HyBECCS). Hence, a procedure for determining the negative emissions potential is also presented. Moreover, the developed approach can also serve as a guideline for decision makers in research, industry, and politics and might also serve as a basis for further investigations such as implementation strategies or quantification of the benefits of biohydrogen production from organic waste material in Germany.