Brazil is the second largest producer of soybeans, the main crop being exploited in the domestic market. For the export of Brazilian soybeans, it is important to emphasize that logistics bottlenecks in the roads, which have the largest representation in the transport matrix of the country, and the low market share of rails and waterways. The lack of infrastructure in Brazilian ports and terminals for integration between the modes is an aggravating factor for logistics integration. Ports have an strategic role in the chain representing a fundamental link in the marketing channel. The Port of Santos is the main route of entry and exit of goods from the country and faces many problems in their infrastructure. In this context becomes increasingly important the definition and implementation of improvement projects in Brazilian ports to allow national products be competitive in the international market. This work aims to analyze the handling of soybeans in the Port of Santos, through the technique of Modeling and Simulation, using specialized software. Therefore, it was necessary to build a solid base of information about the extension of the problem and the Baixada Santista logistic system characteristic. From this point, it was possible to develop and validate the model. With the validated model, scenarios were tested, and among the simulated scenarios, some stand out as possible to improve the handling and export of Brazilian soybeans.