In this work we performed a spectroscopic characterization of natural amethyst, citrine, and prasiolite samples from different localities. These materials were examined by X-ray powder diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), UV–visible spectroscopy (UV–vis), electron paramagnetic resonance (EPR), and inductively coupled plasma atomic emission spectrometry (ICP-AES). Samples were used in this study in as-received, gamma-irradiated, UV-irradiated, and heat-treated conditions. We observed the changes in the FTIR, UV–vis, and EPR spectra of these samples as a function of the condition they were analyzed. We noticed that gamma radiation had a great effect on the color of amethyst and citrine samples used in this work. It was observed that light colored samples showed a deepening of their colors upon gamma-irradiation and a bleaching upon heat treatment at 450°C. However, we observed that gamma radiation had a slight effect on the color of citrine. UV-irradiations revealed that the coloration of both amethyst and prasiolite can be bleached by UV radiation. On the other hand, the color of citrine was not affected by UV radiation.