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Soybean biodiesel (B100) has been playing an important role in Brazilian energy matrix towards the national bio-based economy. Greenhouse gas (GHG) emissions is the most widely used indicator for assessing the environmental sustainability of biodiesels and received particular attention among decision makers in business and politics, as well as consumers. Former studies have been mainly focused on the GHG emissions from the soybean cultivation, excluding other stages of the biodiesel production. Here, we present a holistic view of the total GHG emissions in four life cycle stages for soybean biodiesel. The aim of this study was to assess the GHG emissions of Brazilian soybean biodiesel production system with an integrated life cycle approach of four stages: agriculture, extraction, production and distribution. Allocation of mass and energy was applied and special attention was paid to the integrated and non-integrated industrial production chain. The results indicated that the largest source of GHG emissions, among four life cycle stages, is the agricultural stage (42–51%) for B100 produced in integrated systems and the production stage (46–52%) for B100 produced in non-integrated systems. Integration of industrial units resulted in significant reduction in life cycle GHG emissions. Without the consideration of LUC and assuming biogenic CO2 emissions is carbon neutral in our study, the calculated life cycle GHG emissions for domestic soybean biodiesel varied from 23.1 to 25.8 gCO2eq. MJ-1 B100 and those for soybean biodiesel exported to EU ranged from 26.5 to 29.2 gCO2eq. MJ-1 B100, which represent reductions by 65% up to 72% (depending on the delivery route) of GHG emissions compared with the EU benchmark for diesel fuel. Our findings from a life cycle perspective contributed to identify the major GHG sources in Brazilian soybean biodiesel production system and they can be used to guide mitigation priority for policy and decision-making. Projected scenarios in this study would be taken as references for accounting the environmental sustainability of soybean biodiesel within a domestic and global level.