A comprehensive 3D numerical model for a pile-cum-raft foundation was developed in the present study. The model accounted for the intricate interactions between the piles, raft, and surrounding soil. The model was validated against existing results in the literature, ensuring its reliability. Various key parameters influencing settlement were systematically examined, including the geometric properties of the foundation—such as pile length, diameter, number of piles, and raft thickness—as well as critical soil characteristics like cohesion and internal friction angle. The soil continuum was represented using the Mohr–Coulomb failure criterion. For comparative purposes, a raft foundation was also modelled and analysed. The findings offer valuable insights for the cost-effective design of foundations, emphasizing the impact of different factors on settlement behaviour. These findings can aid in optimizing pile-cum-raft foundations for practical engineering applications.