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The transport system is one of the main bottlenecks of the world’s largest producer and exporter of soybeans, Brazil. Long-distance truck transportation of grains increases costs, food waste, and CO2 emissions. To handle these problems, the Brazilian government seeks to expand the transportation system through the national transport logistics plan (PNLT), promoting efficient operations. Collaborating on the environmental aspect, this paper proposes sustainable logistic infrastructure for soybean transportation. Investigating the largest grain-producing state in the world, Mato Grosso (Brazil), we show the optimal location for capacitated transshipment terminals untangling the relationship between logistics and sustainability. Besides handling cargo truck costs and CO2 emission, the optimization model considers cities, road distances, transshipment terminals existents, terminals capacities, implementing costs, and locations near waterways and railways. In five scenarios with different combinations of waterways and railways, we contrast the cost of installing terminals and the total road distance traveled under different weights for the environmental components. The results indicate that it is possible to simultaneously obtain the minimum cost of installing transshipment terminals and to reduce emissions by 20% in all analyzed scenarios. We conclude that obtaining strategic solutions at lower costs can be combined with proper environmental responsibility. As contributions, the results allow for advances in the area of sustainable logistics, encouraging the development of new research in Brazil involving the dimensions of sustainability. In addition, the study supports the government’s strategic decisions regarding ongoing discussions on expanding the intermodal soy transport network in the country.