The effect of manganese dopant ions on the growth and faceting of manganese-doped GaN (Mn:GaN) nanowires is reported. Using the chemical vapor deposition method we synthesized high-quality internally doped GaN nanowires with varying concentrations of Mn precursor in the reaction mixtures. In all samples we observed nanowires having three distinct cross-section morphologies: hexagonal, triangular, and rectangular. These NWs were present in different ratios depending on the starting concentration of Mn ions. Using electron microscopies we found that the presence of Mn dopant ions inhibits nanowire growth and that the percentage of triangular and rectangular nanowires increases with increasing concentration of Mn precursor at the expense of hexagonal nanowires. We propose that Mn binding to specific nanowire facets plays a key role in governing Mn:GaN nanowire growth and dopant incorporation. These results allow for the preparation of Mn:GaN nanowires in a truly controlled fashion using the developed methodology and for the studies of Mn:GaN nanowire properties with respect to their structure and morphology.