In 2006, Di Natale regained a spot with the "Azzurri" under new manager Roberto Donadoni and was involved in the UEFA Euro 2008 qualification campaign. He was then called up to the Euro 2008 tournament proper, where he missed a crucial penalty during the quarter-final penalty shoot-out against Spain, who went on to win 4–2 on penalties and later the tournament. Di Natale missed the 2009 FIFA Confederations Cup due to a knee injury, which he incurred on 28 March 2009 in an international match against Montenegro.