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We present a novel algorithm based on the ensemble Kalman filter to solve inverse problems involving multiscale elliptic partial differential equations. Our method is based on numerical homogenization and finite element discretization and allows to recover a highly oscillatory tensor from measurements of the multiscale solution in a computationally inexpensive manner. The properties of the approximate solution are analysed with respect to the multiscale and discretization parameters, and a convergence result is shown to hold. A reinterpretation of the solution from a Bayesian perspective is provided, and convergence of the approximate conditional posterior distribution is proved with respect to the Wasserstein distance. A numerical experiment validates our methodology, with a particular emphasis on modelling error and computational cost.