AbstractThis paper investigates for the first time the effect of soil flexibility in structural topology optimization. The case of a structure resting on an underlying soil is explored. The response of the soil is modeled using the Indirect Boundary Element Method (IBEM). The structure is modeled using Finite Element Method (FEM) and the soil domain is coupled by imposing continuity and equilibrium conditions at the soil‐structure interface. Original soil stress influence functions are derived to model voids in the soil. The optimization is carried out by using the Topology Optimization of Binary Structures (TOBS), a recently developed method that employs sequential integer linear programming and the branch‐and‐cut algorithm. Structural compliance minimization subject to a volume constraint is solved. Selected optimization problems are solved for various soil‐to‐structure flexibility ratios. Results show that the soil flexibility may have a significant impact in both the optimized topology and in the achievable compliance of the structure. Results considering voids on the soil, which increases the soil flexibility, affected the final topology of the structures as well as the optimized values.