Loeffler played quarterback for the Michigan Wolverines from 1993 to 1996. After suffering a shoulder injury that prematurely ended his playing career, Loeffler joined Lloyd Carr's coaching staff at his alma mater as a graduate assistant, and was a part of the Wolverine staff during the 1997 undefeated, national championship season. In 2000, Loeffler was named quarterbacks coach at Central Michigan University. After coaching the Chippewas for two years, Loeffler returned to coaching quarterbacks at Michigan for the next six years.

In 2008, the Detroit Lions of the National Football League hired Loeffler to be a part of their failing offensive staff. However,after only one season out of the college ranks, Loeffler was hired by Urban Meyer to join his staff at Florida. Loeffler served as quarterbacks coach, where in his first season he helped Tim Tebow finish the season ranked 1st in passing efficiency. Tebow left Florida with five NCAA, 14 SEC and 28 UF records.

When Steve Addazio left Florida to become the new head coach at Temple University, he brought Loeffler along as the new offensive coordinator and quarterbacks coach. Under his leadership, the Owls offense improved to the 7th leading rushing offense in the nation (257 yards per game) and 33rd nationally in pass efficiency (142.8). The team finished the season 9-4, ranked 2nd in the MAC East and defeated Wyoming 37–15 in the 2011 New Mexico Bowl (the school's first bowl win since the 1979 Garden State Bowl). Sophomore quarterback Chris Coyer was named the bowl's MVP and finished the season with a 177.4 passer rating.

Loeffler was linked to the vacant offensive coordinator positions at the University of Alabama, Louisiana State University and the University of Wisconsin.

On January 22, 2012, head coach Gene Chizik hired Loeffler to serve as offensive coordinator and quarterbacks coach at Auburn.

Loeffler has experience coaching in 10 bowl games including the 1999 Citrus Bowl, 2000 Orange Bowl, 2003 Outback Bowl, 2004 Rose Bowl, 2005 Rose Bowl, 2005 Alamo Bowl, 2007 Rose Bowl, 2008 Capital One Bowl, 2010 Sugar Bowl and the 2011 New Mexico Bowl.