- In the first episode, Amethyst has a nightmare that her friends can't see or hear her.
- When the girls first use the Power of the Five, their attempt to make Coal cool turns him into ice. The spell would only wear off after he melted, which would kill him.
- Snarf's first appearance is pretty frightening, as he's seen only in silhouette. The girls have no idea who or what he is, but they know he's bad news. His first transformation into an ogre is scary, too.
- Simon's possession of Topaz. She's seen fighting from the inside by banging on her own eye, and her mindscape is a yellow void filled with swirls.
- The walking trees in "The Big Test" capture Ruby and even scare the girls.
Topaz: If Mr. Trollheimer taught us about walking trees, I was absent that day!
- Some of Simon's spells, like the one where he brought mannequins to life and when he imprisoned Onyx in a tree.
- In "Field Trip" the girls and boys are attacked by ghost dogs when the bus breaks down. The dogs, being ghosts, are intangible enough to phase through walls, but can still eat them.
- In "Bringing Back the Magic," the girls have to face a cyclops without their magic, and if they failed to find the right tree in time the Ancients would die.
- Zirconia was turned into a tree for 3,000 years. She was conscious the whole time.
- When Simon tries to turn Onyx into a tree, he at first simply imprisons her within one. Eventually she'd become part of the tree, like what happened with Zirconia.
- The Trollz turning evil in "When Good Girls Go Bad". The scare factor is really ramped up when they freeze Coral, Opal, and Jade with a spell and manipulate them like puppets, and kind, sweet Amethyst tends to get the most disturbing lines.
Amethyst: I know it's wrong to use magic to do bad things... But I just can't seem to help myself anymore.
- The final episode has the girls' anger being enough to set off Trollhiti's volcano, and Amethyst almost falls into it before being rescued.