The recent improvement of infrared image quality has increased the use of thermography as a non-destructive diagnostic technique. Amongst other applications, thermography can be used to monitor historic buildings. The present work was carried out within the framework of the Horizon 2020 European project SHELTER, which aims to create a management plan for cultural heritage subject to environmental and anthropogenic risk. Among the chosen case studies is the Santa Croce Complex in Ravenna (Italy), which is exposed to different hazards, including flooding. The church has a peculiar architecture that develops below the street level, so the internal walls are affected by the deterioration caused by rising humidity. In such a case of advanced degradation, passive thermography cannot be used to its full potential. For this reason, an innovative methodology involving active thermography was first developed and validated with laboratory tests. Secondly, we conducted its first application to a real case study. With this purpose, an active thermography survey with forced ventilation was carried out to enhance different stages of material degradation by means of automatic classification of multitemporal data. These experiments have resulted in a method using an active thermal survey in a high moisture content environment to detect masonry degradation.