Niumatalolo stayed on at Hawaii after his graduation, taking a position as a graduate assistant under Johnson. By 1992, he had been elevated to a full-time assistant position.
Navy
When Johnson left Hawaii to become the offensive coordinator at Navy 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. While the offensive coordinator at Navy, Niumatalolo tutored quarterback Chris McCoy, who set a Division I-A record in 1997 for rushing touchdowns by a quarterback with 20, a record that was broken in 2007 by Florida's Tim Tebow. On December 12, 2009, at the annual Army-Navy football game, Navy quarterback Ricky Dobbs reclaimed the record with 24 touchdowns in the 2009 season.
In 1999, Niumatalolo left Annapolis to become an assistant at UNLV. While there, he called the plays and also worked with the kickoff return unit.
Back in Annapolis
Assistant coach
Niumatalolo returned to Navy in 2002 when he was hired by Johnson, who had just taken over the head coaching job at Annapolis, as the offensive line coach. Niumatalolo's work helped Navy establish a rushing attack that led NCAA Division I-A/FBS in yards per game in four of his first five seasons back at Navy, including an unprecedented three consecutive seasons leading the nation in that category. In 2008, Navy averaged 292.4 yards per game on the ground, leading the nation for the fourth straight year in the category. This rushing game helped Navy football reach a level of success it had not seen in decades. Navy went 45–29 under Johnson and appeared in a bowl game every year from 2003 through Johnson's last season in Annapolis in 2007. The Mids also won the Commander-in-Chief's Trophy, the annual football trophy contested by Navy, Army and Air Force, from 2003 through 2007. The 2006 first-class midshipmen went 8–0 against the other academies during their careers at Navy. The Class of 2009 repeated this achievement during the 2008 season with the seventh straight victory over Army and the sixth straight victory over Air Force. Under Johnson, Navy also ended the Mids' long losing streak against Notre Dame in 2007 with a 46–44 triple-overtime win.
Head coach
Niumatalolo was promoted to head football coach at the Naval Academy on December 8, 2007 by Naval Academy Director of Athletics Chet Gladchuk after Johnson departed for Georgia Tech. Niumatalolo is the 38th head football coach in Naval Academy history. On January 7, 2009, Niumatalolo was given a contract extension, although terms and length of the extension were not released. With Niumatalolo as Navy's head coach, beginning with the 2008 season, the Mids have continued their run of success. Highlights in 2008 included an upset in Winston-Salem over #16 Wake Forest, 24–17, the Mids' first victory over a ranked team in 23 years, and a 34–0 shutout victory of Army. Other highlights of Niumatalolo's years as head coach at Navy include:
Navy defeated Army in each of Niumatalolo's first nine seasons as head coach, not losing to Army until 2016. The 2016 loss ended a streak of 14 Midshipmen wins in the Army–Navy Game, the longest winning streak for either side in the rivalry.
The Midshipmen captured the Commander-in-Chief's Trophy in 2008, 2009 and 2012. They went on to capture the trophy outright in 2013, with a 34–7 win against Army, and recaptured it outright in 2015 with wins over Army and Air Force.
Navy defeated longtime rival Notre Dame in consecutive years, 2009 and 2010, for the first time since the early 1960s. The Midshipmen also defeated Notre Dame in 2016.
Personal
Niumatalolo resides in Annapolis with his wife, Barbara, daughter, Alexcia, and sons, Va'a and Ali'i. Va'a played football at BYU and was a graduate assistant at Hawaii. Va'a is currently the assistant to the director of football operations for the Navy Midshipmen. Ali'i currently plays football at Utah. Niumatalolo's mother, Lamala, died in September 2013, while his brother James died December 29, 2015, in a drowning accident while swimming in the ocean near their hometown of Laie, Hawaii. Niumatalolo is a member of the LDS Church, where he has served as the Young Menpresident in his ward in Maryland. He is one of the six main people featured in the documentary film Meet the Mormons released October 10, 2014. Among other callings in the LDS Church, Niumatalolo has served as a counselor in a bishopric. In January 2019, he was called as president of the church's Annapolis, MarylandStake.