After his third season in Richmond, Johnson was chosen as the general manager of the Kansas City Wizards by Lamar Hunt and Clark Hunt. During his tenure with the Wizards, Johnson made an immediate impact, as Kansas City completed the double by winning both the MLS Supporters’ Shield and the MLS Cup in 2000. Four years later, Johnson and Kansas City once again lifted a trophy in 2004 with a win over the Chicago Fire in the U.S. Open Cup Final. In addition to his tactical and management decision making, Johnson was also instrumental in the transfer of ownership of the club from the Hunt family to OnGoal, LLC.