Singlet fission produces a pair of low-energy spin-triplet excitons from a single high-energy spin-singlet exciton. While this process offers the potential to enhance the efficiency of silicon solar cells by ∼30%, meeting this goal requires overlayer materials that can efficiently transport triplet excitons to an underlying silicon substrate. Herein, we demonstrate that the chemical functionalization of silicon surfaces controls the structure of vapor-deposited thin films of perylenediimide (PDI) dyes, which are prototypical singlet fission materials. Using a combination of atomic force microscopy (AFM) and grazing-incidence wide-angle X-ray scattering (GIWAXS), we find terminating Si(111) with either a thin, polar oxide layer (SiOx) or with hydrophobic methyl groups (Si-CH3) alters the structures of the resulting PDI films. While PDI films grown on SiOx are comprised of small crystalline grains that largely adopt an "edge-on" orientation with respect to the silicon surface, films grown on Si-CH3 contain large grains that prefer to align in a "face-on" manner with respect to the substrate. This "face-on" orientation is expected to enhance exciton transport to silicon. Interestingly, we find that the preferred mode of growth for different PDIs correlates with the space group associated with bulk crystals of these compounds. While PDIs that inhabit a monoclinic (P21/c) space group nucleate films by forming tall and sparse crystalline columns, PDIs that inhabit triclinic (P1̅) space groups afford films comprised of uniform, lamellar PDI domains. The results highlight that silicon surface functionalization profoundly impacts PDI thin film growth, and rational selection of a hydrophobic surface that promotes "face-on" adsorption may improve energy transfer to silicon.