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Understanding structure-property relations is essential to optimally design materials for specific applications. Two-scale simulations are often employed to analyze the effect of the microstructure on a component's macroscopic properties. However, they are typically computationally expensive and infeasible in multi-query contexts such as optimization and material design. To make such analyses amenable, the microscopic simulations can be replaced by surrogate models that must be able to handle a wide range of microstructural parameters. This work focuses on extending the methodology of a previous work, where an accurate surrogate model was constructed for microstructures under varying loading and material parameters using proper orthogonal decomposition and Gaussian process regression, to treat geometrical parameters. To this end, a method that transforms different geometries onto a parent domain is presented. We propose to solve an auxiliary problem based on linear elasticity to obtain the geometrical transformations. Using these transformations, combined with the nonlinear microscopic problem, we derive a fast-to-evaluate surrogate model with the following key features: (1) the predictions of the effective quantities are independent of the auxiliary problem, (2) the predicted stress fields fulfill the microscopic balance laws and are periodic, (3) the method is non-intrusive, (4) the stress field for all geometries can be recovered, and (5) the sensitivities are available and can be readily used for optimization and material design. The proposed methodology is tested on several composite microstructures, where rotations and large variations in the shape of inclusions are considered. Finally, a two-scale example is shown, where the surrogate model achieves a high accuracy and significant speed up, demonstrating its potential in two-scale shape optimization and material design problems.