In July 2018, Defiance College announced that it had selected Matsakis as head coach of the Yellow Jackets.

Matsakis spent the three years, 2015 to 2017, as the offensive coordinator at Widener University in Chester, Pennsylvania.

In March 2013, Matsakis was hired as the 17th head coach for the Bethany Swedes in Lindsborg, Kansas. He remained there as head coach for the 2013 and 2014 seasons.

In 2010, Matsakis was hired to be the head coach at Enka High School in Candler, North Carolina where his teams compiled a 13–23 record before resigning in 2013.

During the mid 1990s, Matsakis served as an assistant coach at Hofstra University on Long Island. In 1999, Matsakis served as the offensive coordinator at the University of Wyoming. In 2000, he accepted the position of special teams coach at Texas Tech, where he coached until he became the head coach at Texas State for the 2003 season. Matsakis returned to Capital University when he was hired as the offensive coordinator for his alma mater on February 15, 2008 by new head coach Jim Bickel. Matsakis was hired by the Winnipeg Blue Bombers of the Canadian Football League (CFL) to replace the ill Andy Cox as their running backs coach two weeks into the 2009 season.

Matsakis was the 19th head football coach for Emporia State University in Emporia, Kansas and he held that position for four seasons, from 1995 until 1998. His overall coaching record at Emporia State was 26–18.

Matsakis is a 1984 graduate of Capital University in Columbus, Ohio, where he was a four-year letter winner and a three-time First Team All-Ohio Athletic Conference selection as a kicker. He still currently holds the school record for longest field goal, a 54-yarder in 1981.

Manny Matsakis (born Emmanouel M. Matsakis; April 16, 1962) is an American football coach and former player. He is the head football coach at Defiance College, a position he has held since 2018. Matsakis served as the head football coach at Emporia State University from 1995 to 1998, at Texas State University in 2003, and at Bethany College in Lindsborg, Kansas from 2013 to 2014.