We give a new proof of the Pfaffian-Grassmannian derived equivalence between certain pairs of non-birational Calabi-Yau threefolds. Our proof follows the physical constructions of Hori and Tong, and we factor the equivalence into three steps by passing through some intermediate categories of (global) matrix factorizations. The first step is global Knoerrer periodicity, the second comes from a birational map between Landau-Ginzburg B-models, and for the third we develop some new techniques.