Freight transportation can impact the effectiveness of smart city development if it is not well planned. Commodities with international flows such as soy can cause traffic in urban areas where ports are installed, negatively influencing economic (e.g. delays and fines), social (e.g. population quality of life) and environmental (e.g. intensification of pollutant and greenhouse gases emissions) dimensions. Thus, this paper aims to apply a location-allocation mathematical model to determine the ideal location of logistics integration centers - LICs dedicated to soybean transportation. We believe that, by properly locating structures that allow intermodality, the use of road transport would decrease by replacing it with intermodal alternatives with less environmental impact, reducing road congestion in urban centers under port influence. In addition, the total costs of the network would be optimized, promoting positive economic impacts on the soybean logistics chains. Therefore, eight scenarios were established varying the model's input parameters (such as investment and minimum volume of soybean moved through a LIC). The model was implemented in the Mosel language using the Xpress IVE solver version 1.24.24. The costs of each scenario were investigated, and the benefits related to the currently configuration (with no LIC) were pointed out. In the end, it was observed that the applied model might support government strategic planning (including, here, the design of smart cities).