Green roofs have become a popular sustainable solution in urban areas, and in recent years, shipping containers have gained popularity as a sustainable alternative for housing. A promising proposal is to combine these two solutions. This research aims to analyze the thermal behavior of experimental modules of scale constructions. Four modules were constructed with different substrate thicknesses (4, 6, 8, and 12 cm) to verify the impact on thermal behavior and provide guidance for this technology. Additionally, another module was built without a green roof for control purposes. The indoor and outdoor air temperatures and humidities, soil moistures, and temperatures between green roof layers were recorded in a tropical climate in summer. The behavior was similar between the different thicknesses for the whole period but with significant differences in the indoor temperature amplitudes (13.8 °C for the thinner substrate, 9.7 °C for the thicker one, and 38.7 °C for the bare roof). This study also revealed considerable heat conduction between the side walls and the slab, which resulted in an upward heat flow to the substrate during a day with a clear sky, which is the opposite of what is observed in conventional roofs. During the night and rainy periods, temperatures tend to become closer between the roof’s layers when the substrate dissipates the energy absorbed throughout the day.