The concentration of various contaminants in a plasma can be monitored during processing of a substrate such as a silicon wafer, in order to prevent an unacceptable amount of contamination from being deposited on the substrate. The radiation emitted from the plasma through a window in the processing chamber during processing can be detected and measured by a tool such as an optical emission spectrograph (OES) and the relative intensity of peaks in the spectrum corresponding to various contaminants can be analyzed in order to determine contaminant concentration. In one embodiment, the concentration of aluminum in a plasma is monitored during a plasma chemical vapor deposition (CVD) process in order to ensure that the amount of aluminum in the produced device is lower than a maximum threshold amount.