The 40-year-old formerly played for the Addicks in the 1990s, playing 58 times before moving to Elland Road in 1996.
He returned to Charlton on a temporary basis in January, but as reported by the
The former England player spent time at Watford, with their development squad alongside his former Leeds teammate Harry Kewell.
On returning to coach at the Valley Bowyer said: "
"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 on to the lads. I've worked under a lot of good people in my career and Charlton is where it all started, so it's a bit of a fairytale for me."