Alphys is a yellow, reptilian monster of similar height to the protagonist. Her posture is somewhat hunched over, giving her an appearance of nervousness. She has yellow scales, claws, and protruding teeth (which seem to vary between two and four depending which way she faces). Her feet have three toes while there are three fingers and a thumb on each of her hands. Her "hair" is designed into points facing the back of her head. She normally wears round glasses and a white lab coat. Her glasses do not cover her eyelashes. However, she wears a polka dot dress a friend picked for her on her date with the protagonist.

Alphys is a shy introvert who frequently stutters when she converses. She has low self-esteem, makes self-deprecating comments, and devalues her skills at times. True to her role as a scientist, Alphys is intelligent, analytical, and observant. She occasionally theorizes on matters, and can create thorough plans from them. She can create inventions that use metal and magic, such as a "magical spear repair kit." Alphys is adept in programming, robotics, and mechanical engineering. She is agile when she works a project, and has formal writing when documenting her research.

Alphys is passionate in her work and interests. She often gets excited when sharing her opinions. Alphys's hobbies include enjoying human anime, manga, and video games. Alphys is fond of posting online content, writing walkthroughs for games, though she prefers giving puzzle solutions as a last resort, shipping, and writing fanfiction. Alphys also has crushes on multiple characters of male and female genders. Some of them are mild, such as her crush on Asgore and her compliments towards Toriel, while her most serious crush is Undyne, though she struggles to communicate her feelings.