Methods and systems for calibrating system parameter values of a target inspection system are presented. Spectral Error Based Calibration (SEBC) increases consistency among inspection systems by minimizing differences in the spectral error among different inspection systems for a given specimen or set of specimens. The system parameter values are determined such that differences between a spectral error associated with a measurement of a specimen by the target inspection system and a spectral error associated with a measurement of the same specimen by a reference inspection system are minimized. In some examples, system parameter values are calibrated without modifying specimen parameters. Small inaccuracies in specimen parameter values have little effect on the calibration because the target system and the reference system both measure the same specimen or set of specimens. By performing SEBC over a set of specimens, the resulting calibration is robust to a wide range of specimens under test.