Soybean biomass for biodiesel, produced in Argentina amongst other places, is considered by some to reduce greenhouse gas emissions and mitigate climate change when compared with fossil fuel. To ensure that the production of biofuels is ‘sustainable', EU institutions and national governments are currently designing certification schemes for the sustainable production of biomass. This paper questions the validity of proposed environmental standards, using the production of Argentine soybean as a case study. The production of soybean production is associated with profound environmental impacts. The use of pesticides induces resistance in weeds, leading to an increase in the quantity and variety of pesticides used. Soil fertility is declining due to intense production and soil demineralisation is addressed by the use of synthetic fertilisers, whose production is energy intensive and whose use generates emissions of N2O. The large quantity of substances, sprayed by terrestrial and aerial means, has negative impacts on biodiversity, water, soil, and human and animal health. The intensive production of soybeans also leads to social impacts, including loss of livelihoods and food sovereignty, and a rural exodus. Ultimately, the high demand for soybean is a driver of deforestation and the loss of native habitats that are vital to climate stabilisation. In addition, several studies relate deforestation to the outbreak of vector borne diseases which affect human populations. Emissions from soils have been demonstrated in several studies, but the atmospheric impact of soybean cultivation has not been tested in situ. Some of the models for climate impact (N2O emissions etc) are based on in vitro studies, while field data are scarce. The situation, which is outside the control of the EU, has not been sufficiently researched. Furthermore, there are serious questions regarding the enforcement of environmental legislation in production countries, particularly now EU countries are adopting mandatory blending of fuels. The study considers that a certification system will not create the conditions for environmental sustainability. This is exemplified by soy, whose cultivation undermines the climate benefit claimed for soy-based biodiesel. This paper concludes that to certify soy monocultures as sustainable would exacerbate existing climatic and environmental problems.