The hollow core, concentric graphitic shells, and large surface area of the carbon nano-onion (CNO) make these carbon nanostructures promising materials for highly efficient catalytic reactions. Doping CNOs with heteroatoms is an effective method of changing their physical and chemical properties. In these cases, the configurations and locations of the incorporated dopant atoms must be a key factor dictating catalytic activity, yet determining a structural arrangement on the single-atom length scale is challenging. Here we present direct imaging of individual nitrogen and sulfur dopant atoms in CNOs, using an aberration-corrected scanning transmission electron microscopy (STEM) approach, combined with electron energy loss spectroscopy (EELS). Inspection of the statistics of dopant configuration and location in sulfur-, nitrogen-, and co-doped samples reveals dopant atoms to be more closely situated to defects in the graphitic shells for co-doped samples, than in their singly doped counterparts. Correlated with an increased activity for the oxygen reduction reaction in the co-doped samples, this suggests a concerted mechanism involving both the dopant and defect.