Mean ion energy and ion flux have been investigated in a low‐pressure, radio frequency (rf) magnetron discharge (dual rf excitation plasma) as function of substrate rf power and frequency, plasma excitation rf power and process pressure. Electrical and Langmuir probe measurements were used to determine the self‐bias of the electrodes and time‐averaged plasma parameter, respectively. The energy and flux of ions bombarding the substrate surface can be accurately controlled in the low‐energy range (<50 eV) without affecting the state of the discharge by applying an appropriate rf bias power and frequency to the substrate electrode. A simplified sheath model is used to verify the experimentally obtained linear relationship between substrate rf power and self‐bias of the electrode. The ion flux to both electrodes as well as the mean ion energy to the plasma excitation electrode are controlled by the plasma excitation rf power. The increase in process pressure from 5 to 40 mTorr reduces the ion flux to the substrate without changing the mean ion energy. The plasma parameters and their spatial distribution are strongly affected by the magnetic field, which also determines the ion energy flux distribution on the substrate surface.