The ongoing climate change and policies around it are changing how we design and build homes to meet national carbon emission targets. Some countries such as Scotland are adopting higher-energy-efficient buildings as minimum requirements in the building regulations. While net zero homes might be more energy-efficient and emit fewer operational carbon emissions, we have yet to fully understand the influence on the indoor environment, particularly on indoor air quality (IAQ) and thermal comfort. This study compares the IAQ of three homes in Scotland with equal internal layouts and designs but different building fabrics. The homes represent the minimum Scottish building regulations (2015), the Passivhaus standard and the Scottish 'Gold Standard'. Temperature, relative humidity, PM2.5 and total volatile organic compounds (tVOC) were measured at five-minute intervals for seven months and compared to occupants' subjective responses to the IAQ. All three homes had temperatures above the recommended thresholds for overheating. Measured hygrothermal conditions were within the ideal range 66.4% of the time in the Passivhaus, 56.4% in the Gold Standard home and 62.7% in the control home. Measured IAQ was better in homes with higher energy efficiency, particularly tVOC. For instance, indoor PM2.5 in the Passivhaus were 78.0% of the time below the threshold, while in the standard home the figure was 51.5%, with a weak correlation with outdoor PM2.5 (Passivhaus: B rs = 0.167, K rs = 0.306 and L rs = 0.163 (p < 0.001); Gold: B rs = −0.157, K rs = 0.322 and L rs = 0.340 (p < 0.001); Control: B rs = −0.111, K rs = 0.235 and L rs = 0.235 (p < 0.001)). TVOCs in the Passivhaus were 81.3%, while in the control home they were 55.0%. While the results cannot be generalised, due to the small sample, this study has significant policy implications, particularly in Scotland, exhibiting the importance of IAQ in current building legislation and sustainable assessment methods.