Bowyer resigned from the League One club on Monday after being in charge there since 2018.
During that time he led Charlton to the League One play-offs two years in a row, resulting in Charlton’s promotion to the Championship in 2019.
The 44-year-old, who came through Charlton’s academy as a player too, has confessed it was hard to leave the Valley, though, and it will always hold a place in his heart.
“It was a difficult decision to leave. Everyone knows how I feel about the club,” Bowyer said.
“I could have gone before but I felt it was the right thing to do to stay and help the club through the tough times we’ve been through.
“We had some amazing times and some tough times. It has been emotional leaving. I’d like to thank all the players that I’ve worked with and the staff for the hours and hours of hard work that they did. I also want to thank the supporters. We wouldn’t have had those great memories without them.
“The club is now in a place with a good owner that cares and wants to improve the place and I hope the club can continue to grow. It will always hold a special place in my heart.”