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Zircon occurs in many colors, including red, pink, brown, yellow, hazel, or black. It can also be colorless. The color of zircons can sometimes be changed by heat treatment. Depending on the amount of heat applied, colorless, blue, or golden-yellow zircons can be made.

In geological settings, the development of pink, red, and purple zircon occurs after hundreds of millions of years, if the crystal has sufficient trace elements to produce color centers. Color in this red or pink series is annealed in geological conditions above the temperature about 350.

Because of their uranium and thorium content, some zircons undergo metamictization. Connected to internal radiation damage, these processes partially disrupt the crystal structure and partly explain the highly variable properties of zircon. As zircon becomes more and more modified by internal radiation damage, the density decreases, the crystal structure is compromised, and the color changes.