In 1999 he switched to the K-1 and reached the K-1 500 m semifinals at Sydney in 2000. He became one of the top stars in the sport, winning three consecutive K-1 500 m world championships (2002, 2003, 2005). At the Athens Olympics Baggaley won the silver medal in the K-1 500 m, edged out by Canadian Adam van Koeverden.
In the K-2 race he partnered with Clint Robinson to another silver medal. He was voted the Australian Institute of Sport's Athlete of the Year in 2004. Baggeley returned to win in the K-1 500 m event at Zagreb in 2005 prior to being banned for 24 months for steroid use.