Current approaches to carbon nanotube (CNT) synthesis are limited in their ability to control the placement of atoms on the surface of nanotubes. Some of this limitation stems from a lack of understanding of the chemical bond-building mechanisms at play in CNT growth. Here, we provide experimental evidence that supports an alkyne polymerization pathway in which short-chained alkynes directly incorporate into the CNT lattice during growth, partially retaining their side groups and influencing CNT morphology. Using acetylene, methyl acetylene, and vinyl acetylene as feedstock gases, unique morphological differences were observed. Interwall spacing, a highly conserved value in natural graphitic materials, varied to accommodate side groups, increasing systematically from acetylene to methyl acetylene to vinyl acetylene. Furthermore, attenuated total reflectance Fourier-transfer infrared spectroscopy (ATR-FTIR) illustrated the existence of intact methyl groups in the multiwalled CNTs derived from methyl acetylene. Finally, the nanoscale alignment of the CNTs grown in vertically aligned forests differed systematically. Methyl acetylene induced the most tortuous growth while CNTs from acetylene and vinyl-acetylene were more aligned, presumably due to the presence of polymerizable unsaturated bonds in the structure. These results demonstrate that feedstock hydrocarbons can alter the atomic-scale structure of CNTs, which in turn can affect properties on larger scales. This information could be leveraged to create more chemically and structurally complex CNT structures, enable more sustainable chemical pathways by avoiding the need for solvents and postreaction modifications, and potentially unlock experimental routes to a host of higher-order carbonaceous nanomaterials.