A method of controlling a plasma doping process using a time-of-flight ion detector includes generating a plasma comprising dopant ions in a plasma chamber proximate to a platen supporting a substrate. The platen is biased with a bias voltage waveform having a negative potential that attracts ions in the plasma to the substrate for plasma doping. A spectrum of ions present in the plasma is measured as a function of ion mass with a time-of-flight ion detector. The total number ions impacting the substrate is measured with a Faraday dosimetry system. An implant profile is determined from the measured spectrum of ions. An integrated dose is determined from the measured total number of ions and the calculated implant profile. At least one plasma doping parameter is modified in response to the calculated integrated dose.