The one-time England player made his breakthrough as a player with the Addicks in the 1990s, before embarking on successful career that took in the likes of Leeds, Newcastle and West Ham.
In 1996, he was signed by Leeds United manager Howard Wilkinson for £2.8m, which was a record for a British teenager.
Bowyer was convicted of affray and fined £4,500 in the same year following an incident in a McDonald’s restaurant.
Bowyer was a key player in David O’Leary’s Leeds side that qualified for the Champions League in 1999–2000, and which reached the semi finals of the UEFA Cup in 2000 and the Champions League in 2001.
Following an incident near a Leeds nightclub in January, 2000, in which an Asian student suffered severe injuries, Bowyer and Jonathan Woodgate were charged with causing grievous bodily harm with intent and affray.
An initial trial collapsed in April, 2001 and following a second trial, which ended in December, 2001, Bowyer was cleared of both charges while Woodgate was convicted of affray and sentenced to community service.
In 2005, Bowyer agreed a £170,000 out-of-court settlement of a civil action for damages brought by the victim and his brother, who had been less seriously hurt in the assault.
After Bowyer’s acquittal, Leeds fined him four weeks’ wages for a breach of the club’s code of conduct. Bowyer took exception to the fine and was placed on the transfer list.
The dispute was later settled but Bowyer rejected a new five-year contract. A £9m fee was agreed for a move to Liverpool, which fell through but, in January, 2003, Bowyer signed for West Ham before moving to Newcastle, returning to the Hammers and going on to play for Birmingham and Ipswich.
Now 40, Bowyer returned to Charlton on a temporary basis in January but manager Karl Robinson has moved to promote him to his full-time assistant.
“It feels great to be asked to do this and to work alongside Karl and I’m really looking forward to it,” said Bowyer, who played 58 times for Charlton.
“It was an easy decision to make. We worked closely towards the end of last season so I know the ins and the outs and it’s felt a bit like a homecoming because there are a few faces who are still here from when I was a kid.
“I have a lot more experience now that I can pass onto the lads.”