This study quantified fugitive methane (CH4) losses from multiple sources (open digestate storages, digesters and flare) at two biogas facilities over one year, providing a much needed dataset integrating all major loss pathways and changes over time. Losses of CH4 from Facility A were primarily from digestate storage (5.8% of biogas CH4), followed by leakage/venting (5.5%) and flaring (0.2%). At Facility B, losses from digestate storage were higher (10.7%) due to shorter hydraulic retention time and lack of a screwpress. Fugitive emissions from leakage were initially 3.8% but were reduced to 0.6% after the dome membrane was repaired at Facility B. For biogas to have a positive impact on greenhouse gas emissions and provide a low-carbon fuel, it is important to minimize fugitive losses from digestate storage and avoid leakage during abnormal operation (leakage, roof failure).