Studies have identified seasonal differences between the indoor environment and residents’ comfort, as well as an association between indoor air quality (IAQ) and residents’ overall health. Furthermore, measured IAQ is not always aligned with perceived IAQ. The HOME-Health study is a cross-sectional study with seasonal measurements of IAQ amongst residents living in social housing. The aim is to describe and analyse measured and perceived IAQ, and residents’ health symptoms. We found a lower relative humidity, temperature (TP) and air change level (h−1) level, and a higher carbon dioxide (CO2) level during winter compared to summer. In general, higher IAQ levels were measured in apartments with increased crowdedness. The inability to be able to create cross ventilation increased TP, and a larger number of rooms decreased TP. Overall, there was no clear alignment between measured and perceived IAQ, but we found a trend that higher CO2-levels led to a perception of poor IAQ especially during summer. Overall, draught and thermal discomfort were the most common complaints. Self-reported humidity was increased during winter and was associated with nasal and respiratory symptoms, whereas self-reported humidity during summer was associated with fatigue and dermal symptoms. Findings show challenges with IAQ in Danish social housing that are associated with negative health issues.