Thin-film photovoltaic (PV) devices can be fabricated using a solution-based synthesis procedure in which metal-chalcogenide nanocrystals with aliphatic coordinating ligands are suspended in a solvent to produce a printable ink (NC-ink). However, the aliphatic ligands that are used to solubilize and stabilize the nanocrystals operate as a significant source of carbon impurities that are incorporated into the final device absorber layer. Despite the ubiquity of this technique and the fact that carbon defects have been reported to be found across a spectrum of devices, the structure, properties, and influence of the carbon on PV device performance remain relatively unexplored. Our findings indicate that these organic ligands undergo a pyrolysis reaction during annealing, producing an electrically conductive, graphitic carbon that also reacts with chalcogens (S or Se) to produce heterocyclic moieties. In this work, we used oleylamine (OLA) and dodecylamine (DDA) to fabricate Cu2ZnSn(SxSe1–x)4 (CZTSSe) photovoltaic devices from a NC-ink. DDA, which has fewer carbon atoms and contains no double bond, produces CZTSSe devices with less carbon in the absorber layer; but this reduced carbon content does not translate to improved device performance. OLA, which is a larger molecule and contains one double bond, produces CZTSSe devices with more carbon in the absorber layer. However, OLA also produces more crystalline graphitic carbon and allows for the CZTS nanocrystals to grow to a larger size during annealing, which improves device performance significantly.