So your amethyst crystal has developed some dark spots, huh? Don’t worry, it’s totally normal and not something you did. Those black spots on your amethyst are inclusions of iron and manganese that were trapped inside the crystal as it formed.

While the spots may affect the appearance and transparency of your amethyst, they do not impact its metaphysical properties or ability to energize your space. The black spots are a natural part of the crystal and actually show its authenticity and connection to the Earth.

What Causes Black Spots on Amethyst Crystals?

Black spots on your amethyst are usually nothing serious. The most common causes of the black spots are:

  • Inclusions of other minerals. Amethyst forms over time within rock, and sometimes small amounts of iron or other dark minerals get trapped inside the crystal. These inclusions appear as dark flecks or lines. Not much you can do about this, it’s just part of the natural formation process.
  • Oxidation. If your amethyst was exposed to high heat or bright light for a prolonged period, it may have caused oxidation of the iron within the crystal, resulting in dark splotches on the surface. Keep your amethyst out of direct sunlight and intense heat to prevent further oxidation.
  • Surface stains. The amethyst may have come into contact with other minerals that stained the surface, like soil. Gently scrub the stains with a soft, damp cloth to remove them. For tough stains, use a mild solvent like isopropyl alcohol. Rinse and dry the amethyst thoroughly when done.
  • Cracks. Dark lines inside the crystal could indicate small cracks that formed during the growth process. As long as the cracks do not seem to be expanding or compromising the crystal, they are usually stable and nothing to fret over. However, cracked crystals are more prone to breakage, so handle with care.

The black spots are typically superficial and do not impact the energetic properties of your amethyst. With some TLC, you can often improve the appearance. But avoid over-cleaning, which could do more harm than good. Accept the little imperfections – they give your crystal character and reflect its natural origins.

Are the Black Spots Harmful To My Amethyst?

Don’t worry, the spots are typically not dangerous to the crystal and are usually caused by mineral inclusions or fractures that occurred when the crystal was forming.


Little bits of other minerals can get trapped inside the amethyst during growth, causing dark spots or lines. These inclusions are very common and give the crystal character. They do not affect the crystal’s integrity or metaphysical properties.


Cracks or fractures in the crystal that occurred during formation or handling can also appear as dark lines or spots. Again, small fractures do not necessarily damage the crystal. However, they can potentially become wider over time or with temperature changes. It’s best to avoid any sharp impacts that could worsen existing fractures.

Should You Polish Out The Spots?

Some people prefer the natural, untouched look of a crystal with inclusions and fractures. Others like a smooth, flawless appearance. If the spots really bother you, a jeweler can carefully polish and re-facet the amethyst to improve its clarity and luster. But unless they pose a risk of worsening or falling out, the black spots are usually considered part of the crystal’s natural beauty.

Your amethyst has a story to tell about how it formed over time within the earth. Those little imperfections are a glimpse into its journey and what makes your crystal uniquely yours. Appreciate it for all its natural wonder – spots and all.

How to Prevent and Remove Black Spots on Amethyst

Black spots on amethyst crystals are usually caused by exposure to excessive heat or light. To prevent black spots from forming on your amethyst cluster or point, display it in a spot with indirect lighting away from direct sunlight. High temperatures can also cause black spots, so keep your amethyst in a room with average home temperatures.

To remove existing black spots from amethyst, here are a few gentle methods to try:

  • Gently scrub the black spots with a soft bristled brush like a toothbrush. Rinse your amethyst with water when done to remove any debris. The scrubbing action can help loosen the oxidized layer causing the black spots without damaging the crystal.
  • Create a paste using common household ingredients by combining water with either baking soda or lemon juice. Apply the paste directly to the black spots with a soft cloth or brush. Let it sit for 5-10 minutes, then rinse off with water. The acid in lemon juice or the abrasiveness of baking soda may help lift the black spots from the surface.
  • Soak your amethyst in a mild solvent like isopropyl alcohol, acetone or vinegar for 10-15 minutes. Remove and rinse with water. The solvent helps loosen the bonds between the black spot and the crystal’s surface. You may need to repeat a few times to fully remove spots.
  • As a last resort, you can have a gemcutter or lapidary buff and re-polish the amethyst to remove a thick layer from the surface and eliminate black spots. This is a more extreme measure that will alter the crystal’s appearance and should only be done by a professional with experience working with amethyst and other quartz gems.

Bottom Line

While they may not look as pretty as a flawless, perfectly purple stone, now you know they’re a natural part of the stone’s formation and history. The inclusions give your amethyst character and show its ancient origins deep within the Earth.

Next time you look at your amethyst cluster or tumbled stone, appreciate those black spots and imperfections. They make your amethyst uniquely beautiful and connect you to the cosmic forces that brought those crystals into being millions of years ago. Every amethyst tells a story, spots and all.

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