Fire protection for cultural heritage structures is a challenging engineering task that could benefit from the use of specialized computational tools relying on a performance-based design (PBD) concept rather than on prescriptive-based fire protection codes. In the first part of the present study, the theoretical basis of the proposed computational selection and resource (S and R) allocation model is discussed, related to the assessment of the fire safety index (FSI) and the authenticity preservation index (API). Furthermore, two different multi criteria optimization approaches are proposed to generate optimized fire protection upgrading designs, incorporating the nondominated sorting evolution strategies II (NSES-II) algorithm and the analytic target cascading (ATC) method. In this second part of the present work, the proposed S and R allocation model is implemented in two test cases; Villa Bianca, a famous mansion in Thessaloniki, Greece, and the Monastery of Simonos Petra located in Mount Athos, Greece. Several cases are examined regarding the targeted FSI or API values, taking also into account budget restrictions. In cases where the preservation of the authenticity is considered as an objective within the design process, the need to implement more sophisticated and customized fire protection measures can lead to a significant increase up to almost 200% regarding the total cost, subject to the pursued safety level. Detailed results obtained for each case study are presented and discussed comparatively, demonstrating the efficiency of the proposed S and R allocation model in a wide range of scenarios, as well as its possible utility in multiple applications, facilitating the fire protection design process. Finally, a comparison between the two multi criteria optimization approaches incorporated in the study is also presented and discussed.