We theoretically show how two impurity defects in a crystalline structure can be entangled through coupling with the crystal. We demonstrate this with a harmonic chain of trapped ions in which two ions of a different species are embedded. Entanglement is found for sufficiently cold chains and for a certain class of initial, separable states of the defects. It results from the interplay between localized modes which involve the defects and the interposed ions, it is independent of the chain size, and decays slowly with the distance between the impurities. These dynamics can be observed in systems exhibiting spatial order, viable realizations are optical lattices, optomechanical systems, or cavity arrays in circuit QED.