Beñat Etxebarria grew up 30 minutes from Bilbao in the Basque city of Igorre and joined Lezama in 1998 when he was 11 years old. After rising through the youth ranks he made his first team debut on 29 October, 2006 in a draw against Osasuna but would not feature with the senior squad again as he returned to Bilbao Athletic and was sent on loan to Conquense in 2008. The following year he joined Real Betis and soon became a vital player featuring in over 100 games. In 2013 Athletic paid a reported fee of €8 million to bring Beñat back to the San Mamés where he has inserted himself into the starting lineup and has been an important part of the squad.
Beñat is under contract through 2020 and his deal contains a €50 million release clause.