Egyptian blue and green are among the oldest synthetic pigments produced by humanity. The two pigments are complex multi-phase copper-based systems synthesised with different protocols from the same raw materials. Since the 2000s, synchrotron X-ray techniques have provided significant new insights on their chemistry and microstructure. However, the potential impact of high flux irradiation of these pigments has not yet been studied despite the fact that it can lead to visual discoloration and less readily observable alterations such as defects formation or redox changes. In this work, we investigate the effects of synchrotron X-ray irradiation on Egyptian blue and green samples. Radiation-induced effects are monitored after irradiation at increasing doses using electron paramagnetic resonance (EPR) spectroscopy at temperatures of 290 K and 30 K. The cupric ion (Cu2+) is in D4h axial geometry in Egyptian blue and in disordered geometry in Egyptian green, which makes the two pigments very easily identifiable by EPR. Egyptian green samples are found to be much more sensitive to X-rays than Egyptian blue. In particular, a browning of the green samples is observed from the lowest doses tested while no color change is detected for the blue ones. Three types of radiation-induced defects are detected after irradiation: E′, non-bonding oxygen hole and aluminum hole centers. Correlations between defect intensity and dose are calculated. Archaeological and modern pigments (whether blue or green) do not show the same reactivity to X-rays, which opens the prospect of using radiation-induced defects as a marker of their history.