With their rich historical and cultural significance, churches are particularly vulnerable to earthquakes, as post-event damage assessment has repeatedly shown. This high vulnerability is inherent in their design, as churches were built based on rules of thumb and intended to withstand only static actions. Seismic preservation requires structural analysis, which is essential to accurately assess their safety and determine the need for strengthening interventions. However, churches' complex and irregular geometry makes selecting appropriate modeling strategies challenging, as these must accurately reproduce seismic behavior while keeping computational efforts manageable. This paper addresses this challenge by comparing two nonlinear modeling approaches through modal and nonlinear static analysis on a real case study: the Church of NS Signora delle Grazie e Sant’Egidio in Bussana Vecchia (Imperia, Italy), which suffered severe damage during the 1887 earthquake. The two approaches considered are the Finite Element Method (FEM), based on macro-modeling of masonry as a continuum, and the Equivalent Frame Method (EFM), which simplifies the structure into structural elements such as piers and spandrels. The comparison focuses on pushover curves and dynamic properties to evaluate the reliability of EFM and FEM in capturing the global seismic response. Results show that, despite its simplifications, EFM can provide comparable outcomes to FEM when carefully calibrated and when modeling strategies properly account for the out-of-plane behavior—typically neglected in EFM but implicitly captured in FEM. This suggests that EFM, with thoughtful application, can be a computationally efficient alternative for the preliminary assessment of complex masonry structures like churches.