Structural assessment and seismic vulnerability of ancient masonry buildings is a difficult task even when employing advanced specialized technical skills, which requires a complex study. This paper aims to assess the structural and seismic safety of the Esfahan Shah Mosque in Iran by numerically investigating the nonlinear behavior of the mosque for different scenarios and identifying if there is a correlation between crack patterns resulting from numerical analysis, inspection, and historical evidence. First, the numerical model of the mosque is developed and updated using the experimental parameters obtained from a nondestructive test (NDT) campaign that included ambient vibration and sonic testing. Second, the finite element calibrated model is used to evaluate the structural behavior of the mosque under vertical loading, including the influence of the soil and a sensitivity analysis varying the masonry material properties. Besides, the paper discusses the structural behavior of radial stiffening walls at connect the inner and outer domes of the mosque. Finally, pushover analysis was performed to assess the seismic safety of the building and the efficiency of the structural strengthening implemented in the early 20th century. The different technical observations and analyses lead to a better understanding of the double dome and the eyvan (a rectangular space, usually vaulted, walled on three sides, with one end entirely open) as the most vulnerable parts of the structure, which validates the structural strengthening of the 1930s. Yet, improving the connection between the stiffening walls and the two domes could effectively increase the global structural performance of the building.