Gómez spent eight of the following nine years with Deportivo Alavés, scoring a career-best ten goals in 1995–96 and 1997–98, competing in both cases in the second tier and winning his only piece of silverware in the latter season. He continued to be an important midfield element for the Basques subsequently, contributing to a best-ever sixth-place finish in 1999–2000 with one goal from 34 appearances. The following campaign, he played eight matches in the team's runner-up run in the UEFA Cup, coming on as a 64th-minute substitute for two-time scorer Javi Moreno in the final against Liverpool, lost 5–4 in extra time.