Metroid Prime 2: Echoes began development as a proposal from Retro Studios level designer Tony Giovannini, pitched right after the release of Metroid Prime. Dubbed "Metroid 1.5", the pitch entailed a far different game involving Samus being abducted by a massive alien spaceship out to conquer the galaxy and battling a schizophrenic AI, and far more detailed multiplayer.

The game's Senior Director of Development, Bryan Walker, claimed that he was never able to defeat the Boost Guardian without the use of the game's debug mode.

One of the early tech demos for the Wii in 2005 was a re-tooled version of Metroid Prime 2: Echoes. It was the most advanced of the 8 available demos and was the only game to incorporate the Nunchuk. It took one developer two months to complete the demo for the Tokyo Game Show.