Allowing the transitory attainment of bearing capacity of caisson foundations supporting bridge piers during strong seismic events can lead to substantial optimisation in their design and major cost savings. If the approach of Capacity Design is applied to geotechnical systems, the temporary triggering of plastic mechanisms may be permitted if the resulting permanent displacements are smaller than given threshold values. To validate this design approach, the seismic performance of caisson foundations was assessed through dynamic centrifuge testing on reduced-scale models. This paper presents the results of two tests in which a caisson-pier-deck system was embedded in a typical alluvial deposit and subjected to a series of earthquakes of different intensities. The caissons were founded on soft and very soft clay, to either avoid or induce the attainment of plastic soil behaviour under the same seismic inputs. It is shown that both yielding and failure of the layer of very soft clay limit inertial forces transmitted to the superstructure, validating the design approach and some useful empirical relations available in the literature. On the other hand, inelastic soil behaviour implies accumulation of permanent rotation and settlement of the system, which must be carefully evaluated to check for fulfilment of performance requirements.