In this work, the amorphous part of samples extracted from damaged concrete structural elements of a heritage church of Inousses cluster of islands (Greece) was studied. The samples were obtained from both the interior (dome) and the exterior (two walls and one column) of the church. The techniques employed include simultaneous thermal analysis and solid state nuclear magnetic resonance spectroscopy. Concrete degradation was mainly due to carbonation and it was more intense for the structural elements exposed directly to the environment (external walls and column). The components identified in the sample coming from the external column indicate that a different concrete composition was likely used for its construction.