For historical masonry structures existing in the Mediterranean area, structural strengthening is of primary importance due to the continuous earthquake threat that is posed on them. Proper retrofitting of historical structures involves a thorough understanding of their structural pathology, before proceeding with any intervention measures. In this paper, a methodology is presented for the evaluation of the actual state of historical masonry structures, which can provide a useful tool for the seismic response assessment before and after the retrofitting. The methodology is mainly focused on the failure and vulnerability analysis of masonry structures using the finite element method. Using this methodology the retrofitting of historical structures with innovative techniques is investigated. The innovative technique presented here involves the exploitation of Shape Memory Alloy prestressed bars. This type of intervention is proposed because it ensures increased reversibility and minimization of interventions, in comparison with conventional retrofitting methods. In this paper, a case study is investigated for the demonstration of the proposed methodologies and techniques, which comprises a masonry Byzantine church and a masonry Cistern. Prestressed SMA alloy bars are placed into the load-bearing system of the structure. The seismic response of the non-retrofitted and the retrofitted finite element models are compared in terms of seismic energy dissipation and displacements diminution.