This paper presents the model calibration of three-leaf masonry, illustrated through the case study of the 16th century Saint Mamas Church in Agios Sozomenos, Cyprus. The church, an unfinished structure featuring Gothic and Renaissance architectural elements, has an obscure history and purpose. The absence of relevant documentation and the missing structural components render the church susceptible to environmental and seismic damage. Originally constructed with low-strength materials and empirical techniques that do not comply with current regulatory standards, the church poses significant challenges for engineers tasked with its assessment and retrofit design. Due to the monument's listed status, non-destructive testing techniques were employed to estimate the mechanical properties of the masonry materials, which resulted in an underestimation of the mechanical properties of the stone and mortar. Operational Modal Analysis was then utilized to calibrate the model based on in-situ seismograph results. The study proceeded to the seismic assessment of the church, comparing three types of elastic analysis: equivalent static, response spectrum and time-history analysis. The paper concludes by emphasizing the importance of understanding and preserving historic structures of cultural and architectural significance, like the Saint Mamas Church.