Background: Brazil is one of the largest consumers of fertilizers and is highly dependent on the international market to meet its demand for agricultural production inputs. The complexity of the fertilizer supply chain motivated us to carry out this study on redesigning the fertilizer logistics chain and evaluate strategies for reducing logistics costs by redesigning the fertilizer mixing network in Brazil, a country that is heavily dependent on imported fertilizers for agriculture. Methods: We introduce a multi-product mixed-integer linear programming optimization model encompassing the logistics network, from import ports to mixing factories and agricultural fertilizer supply centers. This model includes logistics infrastructure and taxes, accounting for greenhouse gas emissions (specifically carbon dioxide) in fertilizer logistics. Results: The results indicate that expanding the port capacity for fertilizer importation can significantly reduce logistics costs and greenhouse gas emissions by up to 22.5%, decreasing by 23.9% compared to the baseline. We also observed that removing taxes on fertilizer importation can reduce logistics costs by approximately 11%, but it increases greenhouse gas emissions by 2.25% due to increased reliance on road transport. We identified 15 highly resilient regions for establishing mixing factories, evaluated various scenarios and determined the importance of these locations in optimizing the fertilizer supply network in the country. Moreover, the results suggest a significant potential to enhance the role of Brazil’s Northern Arc region in fertilizer import flows. Conclusions: Public policies and private initiatives could be directed toward encouraging the establishment of mixing factories in the identified regions and increasing transport capacity in the Northern Arc region. Improving the logistical conditions of the fertilizer network would contribute to food security by reducing the costs of essential inputs in food production and promoting sustainability by reducing greenhouse gas emissions.