Historical buildings are important structures and their preservation and restoration is a vital issue worldwide. A crucial step before interventions is the definition of potential hazards and the monument’s vulnerability estimation. The Kapnikarea chapel is one of the most important and popular Byzantine monuments in Athens and dates back to the 11th century. In 1994, construction of the Athens underground Metro system began, with the tunnels passing underneath Kapnikarea foundations. During excavations, sounds of the approaching underground activities (heavy drilling and hydraulic hammer equipment) were heard in the interior of the chapel, and several failures were observed inside the church. Additional reasons reduced the structure’s rigidity are deterioration in time and past severe earthquakes. Towards the restoration planning of the monument, the University of Athens together with the Hellenic Ministry of Culture and Tourism, assigned to our research group the task to investigate the fundamental frequencies of the monument and of its soil foundation in order to determine resonance phenomena capable of compromising building stability during an earthquake. For this purpose, we conducted a microtremor survey. Ambient noise measurements were taken for 87 points located both on the ground and the chapel. Using the HVSR technique we determined the response of the ground, the monument’s predominant frequency and the spatial variations of the peak frequencies on the monument. Based on the experimental observations we discuss the possibility that differentiations are due to the structural members’ particularity and/or health.