[2] When Johnson left Hawaii to become the offensive coordinator at the Naval Academy in 1995, Niumatalolo went with him as the running backs coach.

The following season, Niumatalolo was elevated to offensive coordinator after Johnson left to take the head coaching job at Georgia Southern.

On December 12, 2009, at the annual Army-Navy football game, Navy quarterback Ricky Dobbs reclaimed the record with 27 touchdowns in the 2009 season.

In 2008, Navy averaged 292.4 yards per game on the ground, leading the nation for the fourth straight year in the category.

Under Johnson, Navy also ended the Mids' long losing streak against Notre Dame in 2007 with a 46–44 triple-overtime win.

[9] With Niumatalolo as Navy's head coach, beginning with the 2008 season, the Mids continued their run of success.

The hiring reunited him with his son Ali'i, a graduate assistant with the Bruins, and former Navy director football of operations Bryce McDonald.

[15] He was the acting tight ends coach for the LA Bowl after Jeff Faris was hired by Austin Peay, then was elevated to a permanent position on January 5, 2024.

[15] However, he departed the position two weeks later to accept the head coaching job at San Jose State.

[16] Niumatalolo was named San Jose State's head coach on January 21, 2024, replacing Brent Brennan.