Methods and apparatus for plasma ion implantation with improved dopant profiles are provided. A plasma ion implantation system includes a process chamber, a plasma source to generate a plasma in the process chamber, a platen to hold the substrate in the process chamber and a pulse source to generate implant pulses to accelerate ions from the plasma into the substrate. In one aspect, the pulse source generates implant pulses having pulse widths that are sufficiently long to limit plasma ion implantation during a transient period at the start of each implant pulse to a small fraction of the total implanted dose. In another aspect, ions are generated in a region of the process chamber near a reference potential, such as ground, and are accelerated from the region of plasma generation to the platen. Plasma generation may be enabled after the start of each implant pulse and may be disabled before the end of each implant pulse.