With the growing reliance of indoor living, the design of residential environments has become increasingly critical to ensuring occupant comfort, health, and well-being. This research evaluates thermal comfort variables- air temperature and relative Humidity- in apartment buildings in Amman, Jordan, focusing on their role in mitigating airborne pathogen viability. A simulation-based approach was employed, utilizing Computational Fluid Dynamics (CFD) analysis to assess common apartment design configurations and their impact on indoor environmental quality. The simulation results demonstrate that spatial design directly influences the indoor thermal comfort, revealing significant deficiencies in current apartment layouts. Findings indicate that existing layouts result in low indoor temperatures (16.6°C) and excessive humidity (94.96%), creating favourable conditions for airborne pathogens. Optimizing wall insulation (phenolic foam, R = 5.7, 8 cm) and window-to-wall ratio (40%) significantly improves indoor air quality. The study highlights the need for integrated design strategies to enhance thermal comfort and infection control, supporting policy recommendations for healthier residential environments.