Abstract The paper deals with application of an originally developed methodology for repair and seismic strengthening of St. Clement’s Church, Plaoshnik, Ohrid. To renovate the structure based on the original foundation dating back to the 9th century, complex multidisciplinary investigations were performed in the field of archaeology, conservation, engineering and construction. Presented in this paper are the investigations related to the design of the structural system based on elaborated architectonic bases that are to preserve the authenticity of the structure, performed geotechnical investigations of the site and defined input seismic parameters. A linear-elastic and nonlinear dynamic analysis of the structure was performed. Based on the obtained results, the concept of repair and seismic strengthening of the church was adopted. It consisted of incorporation of horizontal and vertical steel ties in the bearing walls of the structure. This method, which is based on the philosophy of “minimal intervention–maximal protection”, had originally been developed at IZIIS, Skopje and it has been experimentally and analytically verified. The techniques of consolidation of the authentic foundation of the structure and the existing walls with original fresco-paintings are also presented.