In his side’s 2-1 defeat to Swansea last week, the 42-year-old’s language, both on the touchline and in the tunnel area, has come under the spotlight, while he has been accused of questioning the integrity of the referee.
An FA spokesperson said: “Lee Bowyer has been charged with two breaches of FA Rule E3 following the EFL Championship fixture between Charlton Athletic and Swansea City on 2 October 2019.
“It is alleged that the manager’s language – both on the field and in the tunnel area at the end of the fixture – amounts to improper conduct and/or questioned the integrity of the match referee.
“He has until 18:00 on 9 October 2019 to provide a response.”