Ghostfreaks original powers were limited to intangibility and invisibility (accompanied by a inverted color scheme and transparency). It has been explained that he can control his density. He has been shown to be able to change into a smoke like form in Hunted. Ghostfreak can also peel back his own skin, which reveals his horrifying true form, this has been used to terrify Zombozo, fight the giant tick, and as a way for Ghostfreak's inner self to free itself. The original Ghostfreak was granted a second layer of skin to make him usable in sunlight (at the cost of eliminating many of his powers) it is also meant for extreme combat. He was removed from the Omnitrix when he escaped because Ectonurites have the miraculous ability to possess life from a single strand of DNA. He was trapped inside of the Omnitrix again before he was incinerated by Ben in Be Afraid of the Dark.
After having the protective skin removed, Ghostfreak is gained numerous other abilities. He can possess people for limited amounts of time, and gains powerful psychic based abilities such as telepathy and telekinesis (Ghostfreak used telekinesis in the episode Ghost Town while he was fighting Vilgax). Ghostfreak can also shoot a purple or blue beam from his chest (when he pulls back his skin) and from his hands. This ability was confirmed in the episode Be Afraid of the Dark when Benvicktor and Ghostfreak locked beams in the vacuum of space.
Direct exposure to sunlight can greatly harm and even kill Ghostfreak without the second layer of skin (or a host body). This weakness is the result of Zs'Skayr removing his protective second layer of skin after being separated from Ben. Ghostfreak's death happens when Ben opened the roof of a space ship when in space so the light of the sun shined onto Ghostfreak, killing him. Certain substances can also neutralize his phasing ability and his invisibility.