In 1990, Knowles signed with the expansion Illinois Thunder of the National Professional Soccer League (NPSL) He spent two seasons with Illinois, earning NPSL Defender of the Year honors for the 1991–1992 season. That season, he scored forty-five goals in forty games as a defender. In addition to his Defender of the Year Award, Knowles was selected to the first team All NPSL team. The Thunder moved to Denver at the end of the 1991–1992 season, and Knowles played three games there before being traded to the Milwaukee Wave. In the fall of 1993, he tore the anterior cruciate ligament in his right knee. The injury put him out of all but five games of the 1993–1994 season. He bounced back the next season, gaining ninety-four points, making him the second highest scorer on the Wave. He continued his excellent play in the 1995–1996 season, earning his second Defender of the Year title and first team All NPSL recognition while racking up 123 points on 47 goals and 36 assists.