Given buildings’ significant share in global resource use, they have become central to international net-zero targets for 2050. However, the strong focus on energy savings, driven by regulations and densification policies, can sometimes come at the expense of indoor environmental quality (IEQ), as demonstrated by recent investigations into energy-efficient buildings. Using a simulation-based workflow that integrates the EnergyPlus and Radiance engines, validated with measured environmental quality data, this study examines the unintended consequences of current energy efficiency measures on IEQ, focusing on thermal comfort, daylighting, and indoor air quality (IAQ). The analysis is conducted on two exemplar Swiss case studies, identified through a K-means clustering method applied to the Swiss Central Plateau: one office and one residential building. Findings reveal that insufficient daylight, often coupled with overheating episodes, emerges as a dominant issue in standard Swiss buildings. Since IEQ guidelines currently serve only as recommendations and lack regulatory enforcement, the study emphasizes the need for a more balanced and integrated approach to building sustainability, one that gives equal weight to both energy performance and the protection of human health in indoor spaces.