Diamond color centers with applications to single photon sources, quantum computation, and magnetic field sensing down to the nanoscale have been investigated using ensembles of near‐surface implanted atoms. Deterministic ion implantation for ions stopping between 30 and 130 nm deep is demonstrated by configuring an electronic‐grade diamond substrate with a biased surface graphene electrode connected to charge sensitive electronics. The thin graphene electrode has a negligible surface dead layer, so implantation events are signaled from the drift of electron–hole pairs induced by the dissipation of ion kinetic energy in the substrate. Ion beam induced charge maps from a scanned 1 MeV He microbeam show the graphene electrode is highly effective with a charge collection efficiency up to 86% compared to an O‐terminated diamond surface of 30%. For lower energy ions, applicable to near surface implantation, single ion detection confidence is >99(1)% for 19.5 keV H and 85(2)% for 24 keV N ions to allow maps of device surface features by employing a focused ion beam microscope or an atomic force microscope cantilever incorporating a nanostencil beam collimator. In the near‐term, this system can be used to investigate the annealing dynamics for the conversion of single implanted ions into diamond color centers.