Recalling that the series' protagonist, Samus Aran, can morph into a ball, Tanabe was convinced that the Metroid universe could be adapted to a pinball setting.

[1] In addition, new mechanics are introduced, such as enemies that wander around the table, wall jumping, and the ability to fire weapons.

[6] During the course of the game, the player must acquire twelve Artifacts, which are prizes that are awarded after completing objectives such as winning minigames or beating bosses.

[5] To complete the table, twelve different targets must be hit with the balls while they are bombarded by attacks from Meta Ridley, one of the antagonists of the Metroid Prime series.

[5] After the player defeats the Metroid Prime creature on the Impact Crater table, the game unlocks a higher difficulty level, Expert mode.

[10] While making Metroid Prime Hunters, a Metroid first-person shooter video game for the Nintendo DS, Nintendo producer Kensuke Tanabe came up with the idea to make a pinball game based on the Metroid series as Fuse Games finished Mario Pinball Land, another pinball simulator based on a Nintendo property.

Fuse Games then received some assets from Metroid Prime developers Retro Studios,[12] and collaborated with the Hunters team at Nintendo Software Technology to elaborate on specific aspects of Metroid Prime Pinball, such as Samus's wall climbing and shooting abilities.

[12] Named Project Code: Metroid Pinball while in development,[13] the first gameplay footage from the game was released in May 2005, at the E3 convention.

When the Rumble Pak is installed, the Nintendo DS shakes whenever the pinball in the game hits an object.

[14] The tabletops in the game use pre-rendered artwork for graphical effects, including Samus's Morph Ball, which uses renderings of images at several different angles to provide a smooth animation.

This is achieved by touching the Nintendo DS's bottom touchscreen with a finger and pushing it in the direction that the player wants to nudge the tabletop.

[21] Nintendo World Report felt differently; they were impressed with the game's "top-notch graphics and sound that believably invoke the Metroid series".

[32] X-Play felt the same way, noting that the simple controls and "short bursts of gameplay" make Metroid Prime Pinball a perfect handheld video game.

[27] Eurogamer had a different experience, finding that the minigames provided more entertainment than the main game, which they remarked was a "cardinal sin in pinball".