When Mario falls into Goomba Village at the start of Paper Mario, Goombario and his family (Goombaria, Goompa, Gooma, Goomama, and Goompapa) find him and let him rest in the Toad House. When Mario falls off the balcony in Goompa's house, Goompa and Mario find a Hammer and smash through a yellow block to get back to Goomba Village. Kammy Koopa attacks the village and Mario tells them about his quest. Goompa suggests that Goombario join Mario on his adventure, and he accepts. By pressing C-Down, Goombario can use his tattle to find out where Mario is and tell him about the people they meet. Goombario is named after Mario according to Goompapa.
His name appears in the Mario Golf: Toadstool Tour scorechart. Also in Super Paper Mario he appears as a Catch Card found on the twentieth floor of the Flopside Pit of 100 Trials.