A series of 3D finite element (FE) analyses were performed to estimate the peak penetration resistance of spudcan foundations in sand over clay soil profiles. Elasto-perfectly plastic models following Mohr–Coulomb and Tresca failure criteria were used for sand and clay layers, respectively. The coupled Eulerian–Lagrangian (CEL) approach was used to simulate the large deformation in soil that occurs during the spudcan penetration. The performance of the numerical model was validated against centrifuge test results. A parametric study with a broad range of strength parameters for sand and clay was performed. The numerical results were used to assess the influence of sand thickness (Hs), the diameter of spudcan (D), friction angle of sand, and undrained shear strength of clay (su). A wide range of su was utilized to predict the resistance both of the soft and stiff clays. The calculated peak resistances are compared with a published analytical model. It is demonstrated that the model highly overestimates the peak resistance for stiff clays, most likely because it was developed specifically for soft clays and, therefore, does not account for the influence of su. One of the parameters of the model is revised to account both for su. Comparisons highlight that the modified model is able to capture the simulated peak penetration resistance for both soft and stiff clays.