After his 1988 success, Bourbonnais stepped up to the highly popular Formula Atlantic series. Racing in the Atlantic division, opposed to the Pacific debut, Bourbonnais impressed at his debut. In his first Atlantic race, at Lime Rock Park, Bourbonnais won from pole position. The driver, racing a Swift DB4, finished third in the final standings. Improving the following year Bourbonnais won two races. He was the fastest driver at Heartland Park Topeka and again at Lime Rock Park. As Brian Till won three races, Bourbonnais finished second in the championship standings.