The seismic design and retrofitting of new and existing structures often assumes that each structure is isolated from its surroundings. However, significant interaction with nearby structures and the broader built environment can occur. In dense urban areas, it is crucial to carefully consider these phenomena, when analysing seismic conditions. In particular, the seismic effects of interaction between above-ground structures and underground facilities, such as deep excavations for metro stations, must be examined to ensure design is both safe and effective. This paper uses three-dimensional finite element (FE) analysis to examine this issue in the context of the construction of a metro station in a deep excavation in Napoli (Italy) city centre. First, the static construction process was simulated by modelling the excavation and then seismic inputs were applied (with excavation seismic condition). The resulting seismic motion was then compared with that obtained in the absence of the excavation (without excavation seismic condition). Discussion of the results revealed that the main properties of the ground motion, such as intensity and frequency content, can significantly affect the differences observed between the with and without excavation cases, resulting in significant ground motion amplification close to the excavation, with detrimental effect on adjacent existing buildings.