In this paper a phase-by-phase analytical procedure is presented through the case study of St. Panteleimon Church in Thessaloniki, Greece. This procedure follows the historical phases from the structural point of view, i.e. all the basic phases of erection, the partial collapses and the mutilations of the structure during its lifetime. In each phase the background stresses and the hinges created during a preceding phase are taken into account. A simultaneous comparison of the results of the analyses and the historical references concerning partial collapses or heavy damaging is performed. This check enables the verification of the analytical models used. The same concept of modelling and analytical procedure is then used for the analysis of the strengthening measures in their order of application.