Checa continued racing with the factory Yamaha team for the 2003 and 2004 seasons, before he moved to Marlboro Ducati in . In 2006 he returned to the Tech 3 Yamaha team, proving much steadier than in previous years and comfortably beating teammate James Ellison, but was not much a threat to the rest of the field, as they were on Dunlop tyres. He struggled as the sole LCR Honda rider in 2007, with the 800cc Honda proving uncompetitive for many riders. At the Sachsenring Checa got an updated frame, which other non-works Honda riders had found uncompetitive – this is believed to be due to Checa using the same Michelin tyres as the works team, the other Hondas being on Bridgestones.