As a natural, cost-effective, and CO2 storage material, wood has recently gained recognition also in basement constructions. In previous studies by the authors, the hygrothermal behavior of a wooden basement in a reference building in Switzerland was investigated through field measurements and numerical simulations. The measured data were used to analyze the structure’s performance under real operating conditions and to validate the numerical model used for evaluating its long-term performance. Results showed that, under normal conditions, wood moisture levels consistently remained below standard-specified limits, indicating minimal risk of wood decay or mold growth. Furthermore, the validated models in WUFI® Pro and WUFI® 2D were used to conduct risk analyses under critical conditions, evaluating the wooden basement’s hygrothermal performance in various scenarios. This paper presents 2D simulations to investigate the impact of gaps created at the joints between insulation layers, which may occur due to improper workmanship or ground pressure, on the hygrothermal performance of wooden basements. The gap size, indoor relative humidity, and the type of filling material are varied to assess the risk of wood decay in the assembly. The results indicate that, under certain conditions, deterioration may occur in the wooden layer, particularly in the region near the gap. The findings of this study offer practical guidelines for the safe use of wood in the basements, helping ensure durability against moisture-related deterioration.