On 17 June 2019, Bowyer turned down the offer of a contract extension, with the club (and owner Roland Duchatelet) announcing that Bowyer and the club were unable to reach an agreement. However, he later reversed his decision by signing a new year-long deal. In October, he received a three-match touchline ban for "improper conduct and/or questioning the integrity of a match official". Following the club's takeover by East Street Investments, Bowyer signed a new three-year deal on 22 January 2020. Charlton were relegated on the final day of the 2019–2020 season following a 4–0 defeat at his former club, Leeds United.