When caissons are used to support offshore wind substation platforms, the platform and electrical equipment are installed in two phases, with a waiting period of several weeks to months between the two events. To evaluate the peak resistance during secondary loading phase, this ‘penetration-consolidation-penetration’ process in clay is reproduced by the coupled effective stress large deformation finite element analysis to avoid the severe distortion of elements during installation. The numerical model is first verified by simulating a centrifuge test.A comparison of the initial penetration resistance with the penetration resistance after consolidation shows that the waiting period can cause a dramatically increase in soil strength. And the depth of peak penetration resistance during secondary loading phase is almost equal to the initial installation, implying that only a small displacement is required to achieve the compressive ultimate limit state of the caisson after the waiting period. Parametric study is subsequently carried out to investigate the effect of consolidation. A normalized time parameter considering foundation size, soil permeability and consolidation duration is proposed, and a trend line describing the increase of peak caisson resistance with normalized time is provided.