Following Beamer's playing career, he became a graduate assistant at Georgia Tech under George O'Leary. Beamer's team was scheduled to play against his father in the 2000 Black Coaches Association Classic to open the season, but the game was canceled because of lightning and Georgia Tech refused to reschedule it.
In 2004, Beamer was hired by Sylvester Croom at Mississippi State to coach corners where three of his players earned All-SEC Freshmen honors. In 2006, he assumed the role of recruiting coordinator and brought in a class that included former San Francisco 49ers running back Anthony Dixon.
In 2007, Shane was hired by Steve Spurrier at the University of South Carolina to coach outside linebackers and to serve as the special team coordinator. In 2008, the Gamecock defense finished 2nd in pass defense and 13th in total defense nationally. His 2009 special teams unit blocked five kicks, tying for the SEC lead and ranking eighth in the nation, while the Gamecock defensive unit finished third in the SEC in total defense and fifteenth in the nation. In his final two years in Columbia, Beamer also served as recruiting coordinator for the Gamecocks. The 2009 class was ranked 12th best in the nation by Scout.com and Rivals.com and included future NFL draft picks Stephon Gillmore and Alshon Jeffery. Both the 2010 and 2011 recruiting classes ranked in the top 25 and included former South Carolina stars Marcus Lattimore and Connor Shaw.
Virginia Tech Hokies
Beamer joined his father in Blacksburg in 2011 as the running backs coach. In his first year, he tutored the school's single season rushing record holder, All-American and ACC Player of the Year, David Wilson. Wilson was subsequently drafted in the first round by the New York Giants. Beamer accepted Wake Forest game plan information prior to Virginia Tech's game against the Demon Deacons in 2014. The information was provided by Demon Deacons radio analyst Tommy Elrod, a former Wake Forest player and assistant coach who was at the center of what became the "Wakeyleaks" scandal. Virginia Tech eventually lost the game 6-3 in overtime after a 0-0 tie in regulation. The accusations came to light in 2016 when Beamer had moved on to an assistant coach position at the University of Georgia. Beamer denies providing the information to the coaching staff or players but was fined $25,000 by Georgia for his part in the scandal.