Amorebieta was founded in 1925 after the disappearance of Sociedad Deportiva Beti-Arin (founded on 2 December 1923). The Zornotzarra club, alongside 21 other clubs in Biscay, joined the Biscayan Football Federation.
In the 1926–27 season, the club made an outstanding campaign in his second competitive year. It had as its main rival FBC Durango, who finished in the top position after a tiebreaker match, after both teams totalled 14 points in the season. Despite finishing second, Amorebieta clinched the first promotion of its history, rising one step inside the Biscayan Regional category to play, the next year, in the Preferente C division.
In 1962–63, Amorebieta played in the Spanish Amateur Championship semifinals against Real Madrid's farm team, losing 0–2 in Vallecas and managing a 2–2 draw in the second leg, thus being eliminated.
Eighteen years later, the team finished second in Preferente, and played in a promotion play-off against Mondragón CF, which won 4–3 in the first leg; however, a 2–0 home triumph in the second match promoted, for the second time in its history, the club to the fourth division, where it remained for the following three decades.
Perhap's Amorebieta's most successful former player is Xabier Etxeita, who began his career at his hometown club before moving on to Athletic Bilbao, where he was a winner of the 2015 Supercopa de España and was capped by Spain. Amorebieta have close ties with Athletic, and several players have appeared for both clubs.