In recent years, advanced numerical models and high-performance computing have facilitated the utilization of ground motion time series in the assessment of the non-linear dynamic behavior of historic masonry structures. Since recorded accelerograms can be sparse for specific analysis conditions, stochastic ground motion simulations have become a viable alternative to overcome this limitation. This study simulates the recorded acceleration time series of the Central Italy 2016 earthquake event at the closest station to the town of Macerata using a site-based stochastic approach. The simulated motions are seismologically evaluated using a goodness-of-fit method in terms of various intensity measures. The simulated records, in conjunction with real records, are used to study the non-linear dynamic behavior of San Filippo Neri church located in Macerata. The church of San Filippo represents an important example of Baroque religious architecture in central Italy, which was damaged and closed off to the public after the 2016 earthquake events. The construction was investigated with a vast diagnostic campaign which included on-site testing and dynamic identification tests. The collected data is used to calibrate the dynamic response of a three-dimensional finite element model of the church. The model is finally used to compare the non-linear seismic responses under real and simulated ground motions with the site recorded damage. The results of structural responses demonstrate a strong agreement between the real and simulated records, providing evidence to support the validation of the site-based stochastic simulation.