The peak positions of EDS spectrometers should be calibrated so that the positions of characteristic X-ray lines are found within 10 eV of the tabulated values. A miscalibrated system will shift X-ray peaks to improper energies, increasing the risk of misidentification. On the other hand, due to the possible drift of the electronics of the EDS systems, the calibration should be checked periodically to ensure the quality of the EDS measurements.

Calibration can usually be done on pairs of two widely separated X-ray lines, for instance:
         i) Overlapping Al K_α lines at ~1.486 keV (namely, with K_α2 at 1.486 keV and K_α1 at 1.487 keV) and overlapping Cu K_α lines at ~ 8.037 keV (namely, with K_α2 at 8.027 keV and K_α1 at 8.047 keV).
         ii) Overlapping Cu L_α2,1 at 0.928 keV and overlapping Cu K_α lines at ~ 8.037 keV.
         iii) Overlapping Cu K_α lines at ~ 8.037 keV and the zero-strobe peak.

For EDS systems on SEMs, the calibration may require increasing the accelerating voltage of the electron beam, and thus the higher energy X-rays can be generated and recorded.