The paper highlights the potential of cross-docking to reduce storage time and costs. The study addresses evolving market demands that push logistics providers to adopt new technologies for operational efficiency, emphasizing the often-overlooked importance of optimizing cross-docking layouts. The research, conducted in two phases, first analyzed the current warehouse layout (Variant I) to identify inefficiencies and then designed a new layout (Variant II) that was simulated using FlexSim 2022 software. The results showed significant improvements with the new layout, including a 35% increase in deliveries and a 3.23% reduction in forklift travel distances, leading to lower operational costs. Even minor adjustments in the warehouse design proved to enhance logistics efficiency, particularly during peak demand periods like holidays. The study demonstrates how FlexSim software can be applied in cold chain logistics to optimize warehouse operations, underscoring the benefits of cross-docking for cost-effective logistics management.