The Mosque-Cathedral of Córdoba is a complex heritage structure shaped by successive Islamic expansions and the later insertion of a Gothic-Renaissance crossing. The superposition found in this UNESCO World Heritage Site produced significant discontinuities in geometry, materials, stiffness, and load-transfer mechanisms. Understanding the dynamic interaction between the Renaissance structure and the surrounding Islamic mosque is therefore essential for assessing the seismic behaviour of the monument. A finite element model of the crossing and its interaction with the adjacent mosque was developed using shell elements. The model reproduces the main structural components and the geometric configuration of this hybrid part of the building. Dynamic analyses were performed in both main directions of the building to evaluate its structural response under different earthquake input motions. The analyses focused on the distribution of displacements, stresses, and dynamic demands. The simulations reveal a non-uniform dynamic response associated with the differences between the two structural systems. Localised stress concentrations and response irregularities are identified near the contact zones between the upper part of the crossing and the lower mosque. The study confirms the importance of considering the interaction between different historical construction phases when evaluating the seismic behaviour of a heritage monument. The identified zones should be examined in greater detail, as they may represent critical areas for structural vulnerability.