Muniain took part in 58 games overall in 2011–12, scoring on nine occasions as the "Lions" reached both the Europa League and the Copa del Rey finals. In early 2012, he was linked with a move away from Athletic, although a move never materialised as he did not push for a move with three years still left on his contract. He scored just once in 33 league appearances the following campaign, netting the only goal on 10 March 2013 in a home win over Valencia which eased doubts over a possible relegation battle.