Matos competed in the full 2009 IndyCar Series season for Luczo-Dragon Racing. He qualified third in his second race, the Long Beach Grand Prix and finished eight. He was the fastest rookie qualifier in his first Indy 500 and ran in the lead pack, but had a crash with Vítor Meira in which Meira was injured. Matos finished 22nd. Matos captured seasonal Rookie of the Year honors by a wide margin over former F1 driver Robert Doornbos. Matos' best finish was 6th at the Milwaukee Mile. He was running at the finish of each of the last ten races of the season, consistency that led to 13th in the championship despite few top ten finishes. Raphael qualified 12th in both the 2009 and 2010 Indy 500 and he also crashed in both races in roughly the same location at the exit of turn 1. He failed to qualify the AFS entry for the 2011 Indianapolis 500.