The protection of cultural heritage against earthquake induced actions is one of the main challenges the earthquake engineering science and practice are facing. This article presents a seismic assessment study on one of the most ancient colonial buildings present in Peru, the Cathedral of Lima, focusing on its towers. A historical review highlighted how these structures, together with the whole Cathedral, suffered intense damage and partial collapse during previous earthquakes. In order to identify the structure main deficiencies, both linear kinematic analyses and nonlinear static analyses have been performed. Different nonlinear finite element models have been created to evaluate the influence of the adjacent walls. Different load distributions have been compared to evaluate how simplified patterns could provide results close to load distributions taken from a modal analysis of the complex. A simple retrofit strategy, consisting on the introduction of steel ties, has also been studied as a reference. Results show good correlation between kinematic and pushover analyses. The construction, when compared to the requirements of the national code for new buildings, results significantly vulnerable, pointing out the need to accept some structural damage even after seismic retrofit.