When a jack-up rig, equipped with skirted spudcans, is installed on competent seabed soil, limited penetrations (less than full base contact) can be experienced. In such a case, there are limitations in the existing guidelines with regard to the calculations of (V-H-M) capacity based on the conventional methods. In this paper, for a jack-up rig installed in the North Sea, experiencing penetrations less than full base contact, the assessment of footing-soil system stability and stiffness under storm load conditions is carried out. Finite element (FE) analyses are carried out by modelling the spudcan in 2D and in 3D (allowing for accurate modelling of the inner skirts). Due to the gap presence, large deformation, updated mesh (UM) analyses are carried out in order to account for increased (V-H-M) bearing capacity developed due to additional penetrations and gained contact area of the underside of the spudcan and the seabed soil. Important conclusions are derived and recommendations given with regard to identifying the governing failure mechanisms and predicting the behavior and capacity in the elevated conditions of the skirted footings suffering limited penetrations during preloading.