On 31 July 2016, Gómez terminated his contract with Athletic and signed a three-year deal with fellow league team Deportivo Alavés just hours later. On 10 September he scored his first goal for the newly-promoted club, netting the second in a 2–1 historic win against FC Barcelona at the Camp Nou. He also started in the final of the Copa del Rey against the same opponent, which ended in a 3–1 loss.