Leeds lost the final 1–0 against Doncaster Rovers, with the goal coming from Howson's failure to mark goalscorer James Hayter. Nevertheless, Howson was voted Leeds' Players' Young Player and Fans' Young Player of the Year at the club's end of season awards and he was also rewarded for his form with new three-year contract, extending by a further year if Leeds win promotion to The Championship. The following season saw high hopes for Howson but he ultimately struggled to find his form. Fabian Delph superseded him as the club's hot young prospect and the team's indifferent form put added further pressure on the young midfielder. Howson remained a regular under McAllister for the first half of the season but the Scot's underwhelming tenure was eventually ended in December after five straight defeat in the league and cup. Blackpool manager Simon Grayson succeeded McAllister and Howson was mostly restricted to substitute appearances for his first ten games. He eventually returned to the side in February, scoring both goals in Leeds' 2–0 victory over Cheltenham Town. He gradually re-established himself as a first team regular with Fabian Delph being moved out to a wide left midfield position. Howson finished the season in a permanent central midfield place alongside Neil Kilkenny and started in both of the club's two unsuccessful play-off semi-finals against Millwall. At the beginning of Leeds' third campaign in League One, Howson was appointed the new Leeds vice-captain and due to the absence of club captain Richard Naylor, took the captaincy for the start of the season. Howson started the season well, creating a solid central midfield partnership with Michael Doyle and leading the team to nine straight wins in all competitions but he lost the armband when club captain Richard Naylor made his return from injury against Carlisle United in late September. Leeds topped the league for much of the first half of the season after an excellent star; losing only once in the league between August and January, running Premier League giants Liverpool close in a 0–1 defeat in the League Cup and reaching the third round of the FA Cup and regional final of the Football League Trophy by the start of the new year. Leeds began 2010 away to arch-rivals and Champions of England Manchester United in the FA Cup. Howson provided a fifty-yard assist for Jermaine Beckford early in the first half as the League One club caused one the competition's greatest ever upsets and Leeds' first victory at Old Trafford in nearly thirty years in a 1–0 victory.