Malta, as a member of the European Union (EU), has pledged to become carbon neutral by the year 2050. Concurrently, the need for thermal comfort for people within places of worship has expanded tremendously in recent years. As a result, prioritizing passive methods over mechanical air-conditioning systems in such buildings is an essential step toward protecting the macroclimate while achieving a sustainable and comfortable indoor environment. Using DesignBuilder-EnergyPlus software, this paper examines the effectiveness of selective passive measures in two free-running church buildings. Results show that certain passive measures alleviate severe high and low indoor temperatures, resulting in a more comfortable environment. Environmental control, on the other hand, present difficult conservation challenges. Historic church buildings were initially built to make use of passive design features for internal comfort, and this study shows that they outperform expectations and, in general, outperform more contemporary church structures.