We hereby report a study on confinement and electron loss dynamics in the magnetic trap of an electron cyclotron resonance ion source using a special multi-diagnostic setup that has allowed the simultaneous collection of plasma radio-self-emission and x-ray images in the range 500 eV–20 keV. Argon plasmas were generated in single- and two-close-frequency heating (SFH and TCFH) modes. Evidence of turbulent regimes has been found: for stable and unstable configurations quantitative characterizations of the plasma radio self-emission have been carried out, then compared with local measurements of plasma energy content evaluated by x-ray imaging. This imaging method is the only one able to clearly separate x-ray radiation coming from the plasma from that coming from the plasma chamber walls. X-ray imaging has also been supported and benchmarked by volumetric spectroscopy performed via silicon drift and high-purity germanium detectors. The obtained results in terms of x-ray intensity signal coming from the plasma core and from the plasma chamber walls permit the estimation of the average ratio: plasma vs. walls (i.e. plasma losses) as a function of input RF power and pumping wave frequency, showing an evident increase (above the experimental errors) of the intensity in the 2–20 keV energy range due to the plasma losses in the case of unstable plasma. This ratio was well correlated with the strength of the instabilities, in SFH operation mode; in TCFH mode, under specific power balance conditions and frequency combinations, it was possible to damp the instabilities, and thus the plasma losses were observed to decrease and a general reconfiguration of the spatial plasma structure occurred (the x-ray emission was more concentrated in the center of the plasma chamber). Finally, a simplified model was used to simulate electron heating under different pumping frequencies, prompting discussion of the impact of velocity anisotropy vs the onset of the instability, and the mechanism of particle diffusion in the velocity space in stable and unstable regimes.