Genetically modified (GM) seeds have had relevant impacts on worldwide agriculture, even with a limited number of essential traits launched in the markets. The focus on platforms crops has favored the combination of traditional breeding, GM insertion, and diffusion in agriculture. One of the remarkable features of the GM traits has been the close link with pest and weed control systems. We investigate the environmental effects due to pesticides for two different GM seeds: insect resistant (IR) cotton and herbicide tolerant (HT) soybeans in a particular period of Brazilian agriculture, 2009–2013. We use a dataset on commercial farms' use of pesticides and biotechnology in Brazil to document environmental effects of GM traits. We explore within farm variation for farmers planting conventional and GM seeds to identify the effect of adoption on the environmental impact of pesticides measured as the quantity of active ingredients of chemicals and the Environmental Impact Quotient (EIQ) index. The findings show that the IR trait reduces application of insecticides by 22% and the associated environmental impact by 20% the environmental impact of insecticides. However, for HT traits, we find that application of herbicides increases by 55.8% and the associated environmental impact by 44.4%, showing a significant increase in the EIQ. The HT results are driven by an increase of less toxic herbicides elevenfold larger than the decrease in less toxic ones, which we interpret as evidence of weak substitutability between herbicides of different toxicity levels. Addressing what happened in the last decade, the paper also presents a view of the transformations in GM usage in Brazil, focusing on the considerable success in adopting stacked genes. Future perspectives point to a more diversified menu of technologies, crops, and adopting countries, going beyond platform crops and more prominent agriculture exporters.