Practical seismic assessment and design of retrofit for the multitude of small ecclesiastical monuments that abound in the Balkans is the subject of this work. Application of the proposed procedures and methodologies are illustrated in an example case study, a small byzantine church located in Western Greece, which is the region with the highest seismicity in Europe. The church, known as the Fragavilla Monastery, had remained almost undamaged for 800 years, until 1993 when the Pyrgos earthquake caused critical damage mainly in the vaults. Linear elastic analysis to the recorded ground motion, capped by a biaxial failure criterion reproduced the developed damage. The same modelling and analysis procedure was subsequently used for assessment of the intended retrofitting measures. Proposed retrofitting measures included mitigation of the undesirable implications of past interventions along with a combination of strengthening schemes with externally bonded AFRPs strategically placed in the structure. The effectiveness of the proposed solutions is gauged by successful reduction of stress intensity in the critical regions and mitigation of stress localization throughout the structure.