The present invention relates to a method of controlling an ion implanter having a plasma power supply AP and a substrate power supply, the substrate power supply comprising: an electricity generator; a first switch SW1 connected between the generator and the output terminal of the substrate power supply; and a second switch SW2 connected between the output terminal and a neutralization terminal; the method including an implantation stage A-D and a neutralization stage E-H. The method also includes a relaxation stage C-F overlapping the implantation stage and the neutralization stage, during which relaxation stage the plasma power supply is inactivated. Furthermore, the neutralization stage includes a preliminary step E-F for closing the second switch, this preliminary step being followed by a cancellation step F-G for activating the plasma power supply AP.