Side‐band resonances were investigated in the radio‐frequency (rf) spectrum of free ions stored in a radio‐frequency quadrupole ion trap. The magnetic resonance signals occur at the center frequency and at the center frequency plus or minus integral multiples of the characteristic ion macromotion frequencies. The experiment was performed on3He+using the ion storage exchange collision technique. Contributions of the side‐band intensity arose predominantly from the standing microwave field inside the cavity. The effect of a small traveling wave component was also included. The microwave field was fed into the trap structure which, in addition to being used for trapping, was also employed as a broad band cavity in the TE013mode. The dependence of the intensity distribution of the side‐band spectrum on different ion motion temperatures and energy distributions of the ions was studied numerically. It was demonstrated experimentally that initially the stored ions have a uniform energy distribution. Since the stored ion cloud samples different microwave fields at different times, the induced perturbation of the microwave field is spread out in frequency and a correlation function approach is suitable to interpret the side‐band spectra. The present experiment was carried out in the microwave region where narrow‐band coherent radiation fields are readily available. However, the same side bands should also occur in the optical spectrum of stored ions and are of interest to laser cooling experiments.