It is difficult to achieve effective doping without inducing structural damage in plasma-assisted processes. In this study, we demonstrate the effects of the plasma condition on the doping and defect formation in graphene. Direct-current ammonia plasma with parallel electrodes is used. We change the electrode configuration and adjust the plasma input power and treatment time to utilize various ion-bombardment energies and plasma doses. The up-cathode system with a powered upper electrode and ground lower anode is more suitable than the traditional down-cathode system for plasma doping. This configuration yields a low-energy ion process and thus suppresses high-energy ion-induced damages. The plasma condition of 0.45 W of power and exposure for 10 s is the most appropriate for doping. The doping level is estimated as 1.80×1012 and 2.07×1012cm−2 according to Raman analysis and electrical characterization, respectively. The structural evolution of graphene and the doping components are investigated via Raman spectroscopy, atomic force microscopy, and X-ray photoelectron spectroscopy. The results provide an effective doping condition for doping nanomaterials without plasma-induced damage.