The reaction of single-component molecular crystal nanorods with a second species to form cocrystal nanorods is described. Single-component crystalline nanorods, composed of 9-methylanthracene (9-MA), are grown in a porous anodic aluminum oxide template. These templated rods are then exposed to a suspension of 1,2,4,5-tetracyanobenzene (TCNB) in water, which slowly diffuses into the 9-MA rods over the course of days. The two species form a 1:1 charge-transfer complex within the rods, which are transformed from crystalline 9-MA into cocrystalline 9-MA/TCNB. The cocrystal nanorods are characterized by electron microscopy, X-ray diffraction, and optical spectroscopy, confirming their highly crystalline structure and the formation of the charge-transfer complex. Attempts to grow cocrystal nanorods directly from a mixed solution were unsuccessful, as were attempts to recreate the single crystal-to-crystal reaction in macroscopic crystals. This work demonstrates how organic nanostructures can support structure-preserving chemical transformations that are impossible in larger crystals.