This work reports a dimethyl ether-driven fractional crystallization process for separating rare earth elements and transition metals. The process has been successfully applied in the treatment of rare earth element-bearing permanent magnet leachates as an atom-efficient, reagent-free separation method. Using ~5 bar pressure, the solvent was dissolved into the aqueous system to displace the contained metal salts as solid precipitates. Treatments at distinct temperatures ranging from 20–31 °C enable crystallization of either lanthanide-rich or transition metal-rich products, with single-stage solute recovery of up to 95.9% and a separation factor as high as 704. Separation factors increase with solution purity, suggesting feasibility for eco-friendly solution treatments in series and parallel to purify aqueous material streams. Staged treatments are demonstrated as capable of further improving the separation factor and purity of crystallized products. Upon completion of a crystallization, the solvent can be recovered with high efficiency at ambient pressure. This separation process involves low energy and reagent requirements and does not contribute to waste generation.