The last Brazilian agricultural frontier known as MATOPIBA, an acronym for the states of Maranhão, Tocantins, Piaui and Bahia, is a region that has stood out in the scenario of modern large-scale agriculture intensive in capital and technology. However, barriers related to the transportation system, especially regarding the high logistics costs, have been negatively impacting this sector. To optimize the performance of this chain, a model for minimizing transportation costs was developed, using linear programming with an origin-destination matrix. The purpose of this paper was to evaluate whether the use of the North-South Railroad has potential as a new alternative intermodal route for soybean export from the MATOPIBA region, in order to minimize the transportation costs and promote the viability of new ports located in the northeast region of the country. This configuration can also contribute to reduce the overload of Santos Port (SP). Two scenarios were proposed based on the 2016/17 harvest of soybeanwhere the first scenario (A) consisted only of road routes, while the second (B), in addition to these routes, incorporated road-rail and road-water way intermodal routes. As a result, total transportation cost was reduced by 30% in scenario B and about half of all cargo was shipped by the new intermodal road-rail route to the Itaqui Port in the Northeast region. This configuration promotes a more sustainable logistics chain for soy, with more rational use of transport modes and decentralization of investments to other regions.