Following his retirement as a player in 1996, Gadowsky spent three seasons as the head coach of the Fresno Falcons of the West Coast Hockey League, leading the team to three straight Taylor Cup playoff appearances. In 1999 he became the head coach of Alaska-Fairbanks and coached the team for five seasons. In 2004 Gadowsky was hired as the head coach at Princeton University. During his tenure at Princeton he led the Tigers to the 2008ECAC Hockey Championship and to back-to-back NCAA Tournament appearances in 2008 and 2009. On April 25, 2011 he became the head coach of the Penn State Nittany Lions men's ice hockey team, becoming the program's first varsity head coach in the NCAA era for Penn State. Gadowsky took over the program starting in the 2011-12 season, during the team's transition from ACHA DI level to NCAA Division I. The team finished the regular season with a record of 27-4 and received a bid to the 2012 ACHA DI National Tournament as the number one seed and ranked first in the ACHA. The team defeated West Virginia 4-1, followed by Oklahoma 6-3 in the first rounds of the tournament before Penn State lost 3-5 to Oakland (MI) in the semifinal round. In first year as head coach of Penn State, the team finished the season with an overall record of 29-5.