In June 2006 Krystkowiak left Montana to take a job as an assistant coach with the Milwaukee Bucks under Terry Stotts. Krystkowiak was responsible for working with the Milwaukee's big men, notably second year players Andrew Bogut and Charlie Villanueva. He was named head coach of the team on March 14, 2007, after Stotts was fired. Stotts had led the Bucks to a 23–41 record during the 2006–07 season. He signed a reported 4-year contract with the Bucks, with an average annual salary of $2 million Krystkowiak's NBA head coaching debut on March 15, 2007, resulted in a 101–90 victory over the San Antonio Spurs.