The aim of this paper is to investigate the seismic behaviour of a shallow foundation of a sugar silo founded on a structured clay deposit. An advanced constitutive model, which can describe the destructuration process in natural clays, has been implemented in a fully coupled finite element code and used in the numerical simulations. Two different input motions are selected form earthquake databases according to the seismic hazard study of the specific site. The modeling results of the dynamic response of the silo are illustrated in terms of signal amplification throughout the deposit, permanent excess pore water pressures and cumulated foundation displacements during the seismic loading.