Born in Birkenhead, Wootton began his career with Tranmere Rovers but joined Liverpool as a 13-year-old, where he worked with Dons boss Karl Robinson, a then-youth coach with the Reds.
The former England Under-17 international returned to his former side Tranmere on loan in September 2010, making his senior debut for the Lilywhites the following month at home to Brighton & Hove Albion.
After making nine appearances and scoring one goal for the Rovers, Wootton returned to Old Trafford and made his Reds first-team debut in Gary Neville’s Testimonial Match, coming on for the ex-England right-back in the 85th minute.
During the 2011/12 season, Wootton spent time on loan in the Championship with Peterborough United and Nottingham Forest, making 14 appearances for the former and featuring 13 times for the latter.
Wootton’s impressive performances while out on loan earned him a chance with the Man Utd first-team the following season, and he made his competitive debut for Sir Alex Fergusons’s side in a Capital One Cup victory over Newcastle United in September 2012.
The defender made three more appearances for United that season, two of which came in the UEFA Champions League, before returning to London Road on loan for the remainder of the 2013/14 season.
In August 2014, Wootton joined Leeds United for an undisclosed fee, penning a three-year deal with the Yorkshire-men. He went on to play 22 times for the Whites in his debut season, scoring one goal.
The following campaign he added a further 32 appearances to his total, before playing 26 times in his third and final year at Elland Road.
Wootton left Leeds at the expiry of his contract and after fielding a number of offers during the summer, opted for a move to Stadium MK just prior to the start of the 2016/17 season.