Existing heritage structures are frequently composed of diverse masonry typologies, corresponding either to various structural members (e.g. arches, walls, piers) or to additions constructed in different eras. The identification of the material properties of the different masonry typologies is usually demanding due to the high cost of the necessary specialized in-situ experimental testing procedures and to the restrictions posed by the cultural value of historical buildings. This lack of information underlines the importance of probabilistic studies considering the uncertainties connected with the evaluation of the material properties. Such activities become essential in studies dealing with the conservation of built cultural heritage against hazardous events, such as earthquakes. This work investigates the seismic vulnerability assessment of large monumental structures with complex geometry. The church of Santa Maria del Mar in Barcelona is considered as a case study, and a representative macro-element of the bay structure is studied against in-plane horizontal loading through pushover analysis. A Monte Carlo simulation is used to estimate the effect of the uncertainties on the material properties, which are considered as random variables. The developed fragility curves express the safety level and the damage expected on the structure for different seismic hazard scenarios.