Ambrose drove the No. 47 Toyota in the 2009 NASCAR Sprint Cup series, after forming a technical alliance with Michael Waltrip Racing and Toyota Racing Development. Ambrose also drove the last 4 races of the 2008 Sprint Cup series in the No. 47 Toyota, after NASCAR agreed to change MWR's car number from No. 00 to No. 47. Ambrose entered Homestead with the No. 47 in the Top 35, earning him a guaranteed start for the first time in his career. However, a bad finish at Homestead put the team back out of the Top 35, so Ambrose would have been required to qualify on time for the first five races of 2009. Eventually, the team earned a Top 35 exemption after a number of teams merged. Ambrose is ineligible for 2009 Rookie of the Year consideration because he ran 11 races in 2008. Ambrose finished 10th in the 2009 Food City 500, despite losing a cylinder with about 100 laps (50 miles) to go. Ambrose would back this Top-10 finish up by posting 4 more in the first half of the season. Ambrose got his second straight Nationwide Series win at Watkins Glen, his second in two years as he held off Kyle Busch for the win. He followed up with a 2nd place in the Sprint Cup race at the Glen. The following week Ambrose dominated the Nationwide race at Montreal, but on the final lap, he was passed by Carl Edwards when Ambrose jumped over the curb too high, and Carl Edwards zipped past him for the win. Ambrose picked up a top ten finish at the 2009 Sharpie 500. Ambrose charged hard from being 1 lap down with less than 100 laps left, to finish in third place behind Kyle Busch and Mark Martin.