Return to St. Cloud State
Motzko became the head coach at his alma mater, St. Cloud State, in 2005. In 2013, his contract was extended through the 2020–2021 season.[6]
On March 26, 2010, Motzko led the Huskies to their first NCAA Tournament win in the West Regional at Xcel Energy Center. SCSU earned a 4–3 victory in double overtime against Northern Michigan University. The victory snapped an eight-game losing streak in the tournament for SCSU. St. Cloud fell in the West Regional Championship game to the University of Wisconsin the next night.
In the 2012–2013 season, Motzko led SCSU to a WCHA regular season championship, the Huskies' first regular season conference title. Though they secured the #1 seed, the Huskies shared the MacNaughton Cup with the University of Minnesota. On March 30–31, 2013, Motzko led the Huskies to a pair of NCAA Tournament victories over Notre Dame (5–1) and Miami University (4–1) at Huntington Center (Toledo) to advance to the first Frozen Four in school history. St. Cloud fell to Quinnipiac University in the Frozen Four on April 11, 2013, at Consol Energy Center.
In the 2013–14 season, Motzko led the Huskies to the inaugural NCHC regular season championship. Unlike in the 2012–13 season, the Huskies held the Penrose Cup alone. On March 29, 2014, Motzko led the Huskies to a win over Notre Dame (4–3 OT)in the NCAA tournament West Regional at Xcel Energy Center to advance to the Regional Championship for the second straight year, but fell to the University of Minnesota 4–0.
In the 2015–16 season, Motzko led the Huskies to a school record-tying 31 victories as well as the first NCHC conference tournament championship in school history, defeating the Duluth Bulldogs 3–1 in the Frozen Faceoff title game on March 19, 2016. The victory also gave Motzko and the Huskies their fourth straight NCAA Tournament berth, also tying a school record; they would fall to Ferris State University (5–4 OT) in the NCAA West Regional at Xcel Energy Center.
In the 2017–2018 season, the Huskies won their second Penrose Cup as NCHC regular season champions. They also qualified for the national tournament as the overall #1 seed.
Return to Minnesota
On March 27, 2018, Motzko was named the 15th head coach of the University of Minnesota, following Don Lucia's resignation.[8] During the 2025–26 season, Minnesota finished with an 11–22–3 record, their worst record since 1972.[9] Motzko and the University of Minnesota mutually agreed to part ways on March 18, 2026, ending his eight-year tenure with the team.[10]