Adobe churches are representative of Andean architectural heritage, yet their structural vulnerability to seismic events remains a significant concern. This study evaluates the seismic performance of the 17th-century Church of Santo Tomás de Aquino in Rondocan, Peru, an adobe building that underwent conservation work in the late 1990s. The assessment combines in situ inspections and experimental testing with advanced nonlinear numerical modeling. A finite-element macro-model was developed and calibrated using sonic and ambient vibration tests to replicate the observed structural behavior. Nonlinear static (pushover) analyses were performed in the four principal directions to identify failure mechanisms and to evaluate seismic capacity using the Peruvian seismic code. Kinematic limit analyses were conducted to assess out-of-plane mechanisms using force- and displacement-based criteria. The results revealed critical vulnerabilities in the rear façade and lateral walls, particularly in terms of out-of-plane collapse, while the main façade exhibited a higher capacity but a brittle failure mode. This study illustrates the value of advanced numerical simulations, calibrated with field data, as effective tools for assessing seismic vulnerability in historic adobe buildings. The outcomes highlight the necessity of strengthening measures to balance life safety requirements with preservation goals.