Adequate management of indoor air quality (IAQ) in healthcare units has relevant impacts on sustainability performance due to its effects on patient safety, occupational health and safety, and energy consumptions. This study sought to identify improvement opportunities on IAQ management by collecting and analyzing experimental data of selected parameters in three healthcare units in Portugal: Two general hospitals and one primary healthcare center. Indoor air temperature, relative humidity, CO2, bacteria, and fungi concentrations were measured in summer and winter campaigns in June/July 2017 and in January/March 2018. Results show that the exclusive use of natural ventilation is not adequate when the affluence of users is high, but the analyzed parameters revealed acceptable results under low occupation intensity conditions. Results also show that keeping low indoor air relative humidity has a significant impact in reducing fungi concentration and that there is a significant correlation at the 0.05 level between indoor air CO2 concentration and bacterial loads. Therefore, as opportunities to improve sustainability, IAQ management in healthcare facilities should consider natural ventilation as a complement to mechanical ventilation systems and should focus on adequate control of indoor air relative humidity and CO2 concentration to reduce the risk of airborne infections.