A site-specific assessment is required to ensure the safe operation of a mobile jack-up unit under a design storm. The evaluation of jack-up structural response strongly depends on an accurate assessment of the interaction between all spudcan foundations and the supporting soils. Macro-element models have been increasingly applied to describe the non-linear spudcan foundation behaviour under combined loading, which can be coupled directly with the numerical analysis of the structure. To address the need to extend the application of the macro-element modelling approach to layered soils, this paper presents example jack-up quasi-static pushover analyses using a newly proposed macro-element model for describing the behaviour of spudcan footings in soft clay overlying sand. When employed within a structural analysis, the macro-element model allows the evolution of the load-displacement response of each individual spudcan as well as the global system response to be examined. The presence of the underlying stronger sand layer is shown to increase the pushover capacity and the system stiffness of the jack-up units. The results emphasize the benefit of using the macro-element foundation model for accurate assessment of the jack-up capacity when subjected to external loading from the ocean's wind, waves and current, which can contribute to the improvement of the site-specific assessment of jack-up units installed in clay overlying sand.