A final row over potential loan signings from the Premier League was thought to have made up the manager's mind even before Sunday's 3-1 defeat at the hands of Birmingham City.
The former England manager had looked uncomfortable from day one of his return to the domestic game, issuing a number of pleas for investment in a squad that was hit with a number of departures over the summer.
Fans backed McClaren over that issue but the strength of his position was undermined by some dreadful performances and results on the pitch.
Chairman Doughty is to step down from his role at the end of the season it has been confirmed although an official club statement has said he will continue to 'support the club financially through the implementation of Financial Fair Play rules.'