In 2006 and early 2007, Johnson suffered a decline in form, scoring only twice in the 2006 MLS season and failing to make an impact with the national team. However, Johnson returned to form with the start of the 2007 MLS season, notching twelve goals and three assists in his first eleven games. On June 2, 2007, Johnson became the first player ever to score back to back hat-tricks in MLS play when he scored three goals against the New York Red Bulls, following a three-goal performance against the New England Revolution the previous week on May 26.