After ending his playing career in 1997, Morton began working for the National Football League's Oakland Raiders, initially in the personnel department. In 2002 he took a coaching position in the organization, as a Senior Offensive Assistant on a team that made it to Super Bowl XXXVII under head coach Bill Callahan. After another year at the position, he was elevated to Tight Ends Coach for the 2004 season under new Raiders head coach Norv Turner. In 2005 he joined Jim Harbaugh's staff at the University of San Diego, a D-IAA college program, where he coached the passing game and wide receivers for a squad that went 11-1-0 and won the Pioneer Football League Championship. The following season he took a position as an offensive assistant with the New Orleans Saints under head coach Sean Payt