The emissions of ten representative agricultural biogas plants located in Germany were investigated to generate a comprehensive inventory of greenhouse gas emissions that occur within the biogas production process. The main methane emission sources were identified by a site inspection with a portable flame ionization detector. Whenever possible, the released amount of methane was quantified by installing a chamber around the identified sources. The chamber was flushed with air, and the values of the flow rate and the measured concentrations in the exhaust allowed the determination of the methane emissions. The two main sources of emissions turned out to be the digestate storage tanks when constructed without a sealed cover and the cogeneration unit. In some cases, improper handling of equipment within the gas‐filled digester headspaces and pipes caused substantial emissions. The results will be used for a comprehensive life cycle assessment of the biogas production process. Finally, sufficient measures for a substantial reduction of emissions will be developed.