Amorebieta was founded in 1925 after the dissolution 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 its 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 semi-finals of the Spanish Amateur Championship 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 was 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 in Group 2 and qualified for the promotion play-offs, 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 more successful, as the club finished eighth.
On 22 May 2021, Amorebieta was promoted to the Segunda División for the first time ever by defeating Badajoz in the final round of the promotion play-offs. Immediately they faced their first problem of where to play, as their basic Urritxe ground did not meet requirements by several measures and would be prohibitive to upgrade, and none of the possible options, including Ipurua in Eibar and Lezama outside Bilbao, was an ideal solution. On 17 June, the club reached an agreement with Athletic for the utilisation of Lezama's ground 2, after it was approved by the LFP.