He spent almost the entirety of his professional career with Athletic Bilbao after making his debut with the first team in 2007, appearing in 507 competitive matches and scoring 56 goals for the club.

On 31 January 2009, he scored four minutes from time to give his team a 3–2 home win against Málaga CF,[7] in an eventual narrow escape from relegation.

[16][17] In September 2016, Susaeta broke the club record for appearances in European competition, passing the total of 55 set in the 1970s by goalkeeper José Ángel Iribar.

[20] The club's final home match involved tributes to him, as well as fellow long-serving squad members Ander Iturraspe and Mikel Rico who were also departing in similar circumstances.

[23] The following 15 January, having made just seven appearances in Japan, he signed for Australia's Melbourne City FC for the rest of the A-League season;[24] he left in mid-July, the delay in his release being due to the COVID-19 pandemic.