Gemstones are often treated to enhance the color or clarity of the stone. Depending on the type and extent of treatment, they can affect the value of the stone. Some treatments are used widely because the resulting gem is stable, while others are not accepted most commonly because the gem color is unstable and may revert to the original tone.

Heat can improve gemstone color or clarity. Most citrine is made by heating amethyst, and partial heating with a strong gradient results in ametrine - a stone partly amethyst and partly citrine. Much aquamarine is heat treated to remove yellow tones, change the green color into the more desirable blue or enhance its existing blue color to a purer blue.

Nearly all tanzanite is heated at low temperatures to remove brown undertones and give a more desirable blue/purple color. A considerable portion of all sapphire and ruby is treated with a variety of heat treatments to improve both color and clarity.

When jewelry containing diamonds is heated(for repairs) the diamond should be protected with boracic acid; otherwise it could be burned on the surface or even burned completely up. When jewelry containing sapphires or rubies is heated(for repairs) it should not be coated with boracic acid or any other substance, as this can etch the surface; it does not have to be "protected" like a diamond.

Most blue topaz, both the lighter and the darker blue shades such as "London" blue, has been irradiated to change the color from white to blue. Some improperly handled gems which do not pass through normal legal channels may have a slight residual radiation, though strong requirements on imported stones are in place to ensure public safety. Most greened quartz (Oro Verde) is also irradiated to achieve the yellow-green color.

Emeralds containing natural fissures are sometimes filled with wax or oil to disguise them. This wax or oil is also colored to make the emerald appear of better color as well as clarity. Turquoise is also commonly treated in a similar manner.

Fracture filling has been in use with different gemstones such as diamonds, emeralds and sapphires. More recently (in 2006) "Glass Filled Rubies" received a lot of publicity. Rubies over 10 carat (2 g), particularly sold in the Asian market with large fractures were filled with lead glass, thus dramatically improving the appearance (of larger rubies in particular). Such treatments are fairly easy to detect.