Biodiesel is an important bridging biofuel for reducing greenhouse gases (GHG). In 2015, Germany introduced a new GHG based quota scheme for biofuels. However, the use of default GHG values for rapeseed cultivation could provide inaccurate for specific regions and locations. Therefore, the aim of this paper was to use RELCA (a REgional Life Cycle inventory Approach) to assess the regional and spatial variation of GHG emissions associated with biodiesel production in Central Germany and to compare these results with the default values of the Renewable Energy Directive (RED), as well as to identify potential mitigation options for biodiesel production. The RELCA simulations indicated GHG emissions of 31.9–39.83 CO2eq./MJ, with emission magnitude changing between biodiesel configurations due to their locations within the CG region. In comparison with typical RED values for biodiesel, the CG simulations showed 13–31% greater mitigation potential. The results also indicated that the configuration of biomass and conversion plant needs to be assessed to develop the most appropriate mitigation strategies. Current GHG mitigation strategies are limited to the energy sector, allowing leakages within the agricultural sector. Therefore, for more spatially targeting GHG accounting to be implemented, sustainability certification should be expanded to other biomass markets.