Biogas production in small-scale plants is considered to be an appropriate technology for energy supply to rural households. It is being beneficial to the environment through replacement of traditionally used cooking fuels (fuelwood and liquified petroleum gas) and so possibly resulting in the reduction of global warming potential. The problem of biogas loss due to leakage or intentional release results in direct methane emissions, threatening to neutralize the environmental benefits of biogas use. The objective of this study was to quantify the impact of partial replacement of traditional cooking fuels by biogas from two most prevalent sizes of biogas plants (BGPs) (6 m3 and 9 m3). The two-phase data collection performed in central Vietnam included semi-structured interviews with biogas plant owners, masons and biogas facilitators. The quantification of Global Warming Potential (GWP) from small-scale biogas plants accounted for four different scenarios: 1. Original scenario (before biogas implementation), 2. Current state scenario (after biogas implementation with reported 40% loss of biogas), 3. Zero-loss scenario (after biogas implementation without biogas loss) and 4. Optimal scenario (the exclusive use of biogas). Currently, biogas covers over 60% majority of cooking energy mix of surveyed households. Households’ consumption of traditional fuels (fuelwood and liquified petroleum gas) was reduced on average by 58% for fuelwood and 65% for LPG. In comparison of Original and Current state scenario, GWP was reduced on average by 11%, suggesting that in the current state, reduction of GWP due to biogas use is under its potential. Two potential scenarios (Zero-loss and Optimal) resulted in the significant GWP reduction, however their achievement is rather theoretical. The break-even point of biogas loss was determined at 53–55%. The findings illustrate the unfulfilled potential of GWP reduction by using biogas and emphasize the problem of significant biogas loss, compromising the environmental benefit of biogas plants.