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.
On 29 May 2011, Amorebieta promoted for the first time to Segunda División B after beating CD Manacor in the 2011 Tercera División play-offs. In its first season in the third tier, the club finished in the fourth position of the Group 2, qualifying for the promotion play-offs to Segunda División, but was eliminated in the first round by Balompédica Linense. In the 2017-18 season Amorebieta finished in the 14th position in Segunda División B, Group 2. The following 2018-19 campaign was much more successful, as the club finished 8th.