Fernández started his season at the 2012 Finlandia Trophy where he won the bronze medal. His first Grand Prix event of the season was Skate Canada, where he beat defending Skate Canada and World champion, Patrick Chan, to take the gold medal. Fernández became the first Spaniard to win a gold medal in the Grand Prix series. Despite his fourth place at the 2012 NHK Trophy, he qualified for the Grand Prix Final. He finished fourth overall at the final after winning the free program with a 4S-3T jump combination, 4S, and 4T. He became the second European to execute three quads in one program — the first being Brian Joubert who landed a 4T-2T combination, 4T, and 4S at the 2006 Cup of Russia — and the first European to do so with a quad-triple combination.