This paper presents the probabilistic seismic performance and loss assessment of an actual bridge– foundation–soil system, the Fitzgerald Avenue twin bridges in Christchurch, New Zealand. A two-dimensional finite element model of the longitudinal direction of the system is modelled using advanced soil and structural constitutive models. Ground motions at multiple levels of intensity are selected based on the seismic hazard deaggregation at the site. Based on rigorous examination of several deterministic analyses, engineering demand parameters (EDP’s), which capture the global and local demand, and consequent damage to the bridge and foundation are determined. A probabilistic seismic loss assessment of the structure considering both direct repair and loss of functionality consequences was performed to holistically assess the seismi risk of the system. It was found that the non-horizontal stratification of the soils, liquefaction, and soil–structure interaction had pronounced effects on the seismic demand distribution of the bridge components, of which the north abutment piles and central pier were critical in the systems seismic performance. The consequences due to loss of functionality of the bridge during repair were significantly larger than the direct repair costs, with over a 2% in 50 year probability of the total loss exceeding twice the book-value of the structure.