After retiring as a player, Bowyer began his coaching career working part-time at Ilkeston, before being appointed as Under-17 coach at Derby County, where he spent six years as an academy coach. He then became Under 18's coach for Blackburn Rovers in 2004. He became Reserve Team manager in 2008, and in December 2012 he was appointed as caretaker manager following the dismissal of Henning Berg, steering them to a 3–1 victory over Barnsley in his first game in charge. It was later announced that Bowyer would remain in charge until the end of January.
Bowyer was re-appointed Caretaker Manager on 19 March 2013, following the sacking of Michael Appleton, until the end of the season. However, on 26 March 2013 Bowyer said he was unsure how long he would remain in the position, in case the club hired a new permanent manager, and on 8 April 2013 Bowyer was summoned to India for a meeting with the club's owners.
Bowyer was appointed the permanent manager of Blackburn on 24 May 2013, on a 12-month rolling contract.
In his first full season in charge the club finished 8th in the Championship, narrowly missing out on a play-off position.