We present a homogenization theorem for isotropically-distributed point defects, by considering a sequence of manifolds with increasingly dense point defects. The loci of the defects are chosen randomly according to a weighted Poisson point process, making it a continuous version of the first passage percolation model. We show that the sequence of manifolds converges to a smooth Riemannian manifold, while the Levi-Civita connections converge to a non-metric connection on the limit manifold. Thus, we obtain rigorously the emergence of a non-metricity tensor, which was postulated in the literature to represent continuous distribution of point defects.