Employing a life-cycle assessment approach, this paper studies greenhouse gas (GHG) emissions resulting from biomethane used as transportation fuel. It focuses on both GHG allocation methodologies and uncertainties regarding GHG emissions from biomethane. The goal is to calculate GHG emissions of two types of biomethane used in transportation: that produced from biowaste feedstock and that extracted from dedicated energy crop feedstocks. The effects of allocation methods used for digestate and those of other factors arising during the life cycle of biomethane are studied. The GHG emissions of biomethane produced from biowaste with digestate use are approximately 22 gCO2eq MJ–1; those of biomethane extracted from dedicated energy crops are 61 gCO2eq MJ–1. However, using the substitution method for digestate decreases biowaste emissions by 10 gCO2eq MJ–1 and dedicated energy crop emissions by 22 gCO2eq MJ–1. The highest emissions uncertainties are related to land use change, cultivation processes, digestate use, and technology selections in digestion and upgrading. Using technology with high energy consumption or methane leakages will significantly increase total emissions. On the other hand, use of renewable energy in processes is one option for decreasing total emissions. It appears that biomethane could be produced with lower emissions than previous studies have shown by optimizing production and implementing new technology. The utilization of digestate in replacing mineral fertilizers, resulting in additional GHG emission reductions, is a key issue which should be accorded more attention in the future. For one to achieve reliable results, factors related to biomethane production and allocation methods for digestate emissions should always be chosen on a case-by-case basis.