[2][3] Born in the capital of Madrid, Amaya began his career at local San Cristóbal de los Ángeles.

He joined another team in the community, Rayo Vallecano, in 2002, also serving a six-month loan spell at lowly UD San Sebastián de los Reyes in the Segunda División B.

Amaya signed for Premier League club Wigan Athletic on a three-year contract on 14 August 2009,[5] being joined by Rayo teammate Mohamed Diamé a week later.

[6] He made his debut in a 4–1 defeat at Blackpool in that campaign's Football League Cup on the 26th, scoring his team's goal with a header in stoppage time.

On 20 December 2015, Amaya was on target at the Santiago Bernabéu Stadium, but his team had to play with nine players for more than 60 minutes and were eventually crushed 10–2 by hosts Real Madrid.