For 2012, Hughes signed for Murphy Prototypes, driving their Oreca 03-Nissan alongside Firth and Brendon Hartley in the 24 Hours of Le Mans, and Firth in the European Le Mans Series. His ELMS debut came at the 6 Hours of Castellet, but it would not be a successful one, with the car catching fire during the event. Once more in the Le Mans event, however, mechanical maladies struck, with suspension failure after 196 laps forcing the team to retire from a strong position. A podium at the 6 Hours of Donington, however, would prove to be the team's only point-scoring finish of the season, as the team once more failed to finish at the Petit Le Mans, following an electronics failure after 330 laps. In addition to his ELMS and 24 Hours of Le Mans entries, Hughes returned to the British GT Championship with Team WFR in the Ginetta G50 GT4, being partnered by Jody Fannin. The pairing dominated the GT4 category, winning eight of their ten races on the way to the title, and finishing 84.25 points ahead of nearest rival Zoë Wenham.