High Desert Mavericks
Following his playing retirement, Wakamatsu became a minor league manager in the Arizona Diamondbacks system, managing the Arizona League Diamondbacks in 1997, the Class-A High Desert Mavericks in 1998, and the Double-A El Paso Diablos in 1999. In 1998 he was named Manager of the Year in the California League, after leading the High Desert Mavericks to the playoffs.