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We present a coupling framework for Stokes-Darcy systems valid for arbitrary flow direction at low Reynolds numbers and for isotropic porous media. The proposed method is based on an overlapping domain decomposition concept to represent the transition region between the free-fluid and the porous-medium regimes. Matching conditions at the interfaces of the decomposition impose the continuity of velocity (on one interface) and pressure (on the other one) and the resulting algorithm can be easily implemented in a non-intrusive way. The numerical approximations of the fluid velocity and pressure obtained by the studied method converge to the corresponding counterparts computed by direct numerical simulation at the microscale, with convergence rates equal to suitable powers of the scale separation parameter $\varepsilon$ in agreement with classical results in homogenization.