In this pinball game based on Metroid Prime, Samus gets knocked and rolled around the table in Morph Ball form; the table contains Metroids, which can latch onto her and suck away health. Tables include the surface of Tallon IV, the Space Station, the Phazon Mines, and more can be unlocked by searching for artifacts and collecting bounties, which are found by destroying Space Pirates and other dangerous creatures.

Metroid Prime Pinball is a pinball game with a Metroid theme. Players can collect power-ups such as missiles and super bombs, which can be helpful when defeating bosses. There are also missions to be completed within a time limit; these missions can involve defeating unique enemies that appear on the table or completing tasks such as wall jumping. Completing missions earns either artifacts or special tokens.

The game also features a single-card multiplayer mode. In this mode, up to eight players can play. The game is a race to see who can reach a certain score first. Players lose points if they lose their ball. It is also possible to dump enemies onto opponents' tables to cause trouble for them.