In the autumn of 1986, a 21-year-old Jones became a full-time professional footballer when he was signed by Wimbledon of the First Division, who paid Wealdstone £10,000 for him. He scored in only his second appearance for Wimbledon on 29 November 1986, in a 1–0 win over Manchester United. He was a member of the Wimbledon team which won the FA Cup in 1988, beating league champions Liverpool 1–0 in the final. Wimbledon cemented their status as a formidable First Division side during this time, with Jones making his name as an enthusiastic and uncompromisingly tough midfielder and a leading member of Wimbledon's famed Crazy Gang.