On 4 January 2021, Marcelino was appointed head coach of Athletic Bilbao on a contract until 30 June 2022. In his first three games in charge, he lost against Barcelona in the domestic league and defeated the same adversary and Real Madrid to win the Supercopa de España. He was also on the bench for two Spanish Cup finals in two weeks (the first having been postponed due to the COVID-19 pandemic), losing both.