Crystallization of organic compounds in nanometer-scale channels of controlled pore glass (CPG) and porous polystyrene (p-PS), the latter prepared by etching of the polylactide (PLA) component of shear-aligned PS-PLA diblock copolymers, produces crystals with dimensions that reflect the size constraints imposed by the channels. The nanoscopic dimensions of the organic crystals embedded in the channels result in a substantial melting point depression compared with the bulk, as demonstrated here for 2,2,3,3,4,4-hexafluoro-1,5-pentanediol (HFPD) and (R)-(+)-3-methyladipic acid (R-MAA). The melting points decreased with decreasing channel diameter, consistent with the increasing surface-area-to-volume ratio of the crystals. Furthermore, at these length scales the latent heat of melting decreased with decreasing crystal size. The melting point depression for both HFPD and R-MAA was greater in p-PS than in CPG, which can only be explained by interactions of the nanocrystals and their corresponding melts with the channel walls. Collectively, these discoveries reveal that simplified descriptions used in previous investigations of embedded crystals, which were limited to porous glass matrixes and ignored the influence of the channel walls, do not capture all the factors affecting the thermotropic properties of the embedded nanocrystals.