This paper investigates vertical temperature gradients in warehouse design to ensure optimal storage conditions. In warehouses with ceilings over 10.0 m high, buoyancy-driven warm air often causes significant temperature disparities. This study uses a combination of field measurements and computational fluid dynamics (CFD) simulations to measure thermal stratification. It also examines the impact of mechanical systems, such as ceiling-mounted radiant cooling and floor heating. CFD simulations are validated against field data, showing that destratification cooling systems can reduce ceiling temperatures by up to 4.0 °C in summer. These systems can also raise floor temperatures by 7.0 °C during heating. Field data collected over a year show vertical temperature gradients up to 3.0 °C. However, the temperature difference between ceiling and floor remains below 0.2 °C, keeping indoor temperatures within an ideal range of 20.0–24.0 °C year-round. The study highlights the benefits of combining radiant cooling with floor heating to achieve temperature uniformity. Floor heating scenarios generate air velocities of up to 0.8 m/s, with an average velocity of 0.2 m/s. In contrast, ceiling-mounted cooling systems result in slightly lower air velocities, reaching a maximum of 0.5 m/s and an average of 0.1 m/s. This research is especially relevant for temperature-sensitive products, as illustrated by a case study involving cured tobacco bales. The retrofit proposals ensure optimal indoor conditions and reduce vertical temperature gradients. These findings validate the proposed methodology as a reliable approach for managing temperature variations in warehouses handling temperature-sensitive goods.