In this study, a simplified methodology for the calculation of the balance of greenhouse gas (GHG) emissions and corresponding saving compared with the fossil reference is presented. The proposed methodology allows the estimation of the anthropogenic GHG emissions of thermochemical biorefineries (net emitted to the atmosphere). In the calculation of the GHG balance, all relevant factors have been identified and analyzed including multiproduction, emissions from biogenic carbon capture and storage (Bio-CCS), co-feeding of fossil fuels (secondary feedstock) and possible carbon storage in biomass-derived products (chemicals). Therefore, it is possible to calculate the balance of GHG emissions of a hypothetical thermochemical biorefinery considering different alternatives of land-use, biomass feedstock, co-feeding of fossil fuels, Bio-CCS incorporation and final use of the products. The comparison of the estimated GHG balance with the corresponding fossil reference for each product is of special relevance in the methodology since it is the parameter used in European regulation for the fulfillment of sustainability criteria in biomass-derived fuels and liquids. The proposed methodology is tested using a previously assessed set of different process concepts of thermochemical biorefineries (techno-economic analysis). The resulting GHG balance and saving are analyzed to identify uncertainties and provide recommendations for future regulation. In all process concepts, the GHG savings are above the minimum requirement of GHG emissions for 2018. In the case of incorporating Bio-CCS, cradle-to-grave negative GHG emissions are obtained. However, in order to assess the role of chemical co-production from biomass, they need to be included in future regulation.