Flowey is the first major character that the protagonist encounters. Flowey serves as the main antagonist for the Neutral and True Pacifist routes, and could be considered a deuteragonist within the Genocide Route. He introduces the player to the mechanics of encounters by sharing "friendliness pellets," which are actually harmful bullets, revealing his philosophy of "KILL or BE KILLED." He serves as the final boss of the Neutral Route. 

Flowey is a sentient golden flower. He has a white center, six yellow petals, and a light-green stem. Flowey can show a variety of expressions and can mimic the faces and voices of other characters. He mimics Toriel and Asgore in some situations, as well as his old self at the end of the Genocide Route. He also mimics the protagonist's face before the Neutral Route's final battle.

Initially, Flowey is friendly toward the protagonist. He greets the protagonist with "Howdy!", calls himself "your best friend," and, like his father, uses words such as "golly" at the end of his sentences. When he is not trying to fool the protagonist into trusting him he will stop using pleasantries and insult them.