Optimizing structures leads to enhanced structural performance and material efficiency. Topology optimization has found several applications in the field of civil engineering to achieve sustainable and resilient structures. Various studies present approaches for topology optimization under uncertainty, considering random loads, geometric perturbations or material variation of a homogeneous material, using homogeneous, stationary random fields. However, little research has been done on topology optimization considering uncertainty in stratigraphy of the underlying soil. In this study, an algorithm is presented for the topology optimization of foundation structures considering uncertainty in the stratigraphy. The algorithm is based on using the Coupled-Markov-Chain theory in order to generate modeling domains of the underlying soil from borehole data, which are then utilized in the topology optimization using the SIMP approach. The results of different optimization methods are compared and evaluated, proving the applicability of the algorithm for the topology optimization of foundation structures to improve sustainability.