Abstract This paper presents a 3D finite element Incremental Dynamic Analysis (IDA) study of caisson foundations carrying single-degree-of-freedom (SDOF) structures on clayey soil. The emphasis is given to the interplay between the nonlinearities developed above (superstructure) and, mainly, below ground surface, either of material (soil plasticity) or of geometric (caisson–soil interface gapping and slippage) origin. The study is performed with respect to the static ( F S ) and the seismic ( F E ) safety factor of the foundation and involves SDOF oscillators of varying mass (to account for vertical loading, F S ) and height (relating to moment loading, F E ) founded on similar rigid cubic caissons. Structural nonlinearity is considered through a simplified moment-curvature law and the yield strength is deliberately chosen so that the following three configurations are obtained: (a) a lightly loaded ( F S =5) seismically under -designed (as compared to the superstructure) caisson, (b) a lightly loaded seismically over -designed caisson, and (c) a heavily loaded ( F S =2.5) seismically under -designed caisson. The analysis is performed with several earthquake records, each scaled to multiple levels of intensity. IDA curves are produced for a single intensity measure, (peak ground acceleration, PGA), and appropriate engineering demand parameters (EDP) describing both the maximum and the residual response of the system. The results emphasize a potentially beneficial role of foundation nonlinearities in reducing the seismic demands on the superstructure, but at the cost of residual foundation settlements and rotations.