Founded in 2017 as Club de Fútbol Molina Promesas, a reserve team of CF Molina, the club were renamed to Club de Fútbol Molina Olimpic after Molina became Independiente de Ceutí FC. In 2019, after their promotion to the Preferente Autonómica, the club were renamed to Club de Fútbol Molina. Two seasons later, the club were renamed to Club de Fútbol Molina San Miguel, after establishing a partnership with Escuela de Fútbol San Miguel;[3] the latter club became their reserve team.[4]
On 30 July 2021, it was made official that CF Molina and EF San Miguel merged, creating Unión Molinense Club de Fútbol.[5] On 10 June 2022, after missing out promotion to Tercera Federación, the club acquired Archena Sport FC's place in the fifth tier;[6][7] their place in the Preferente Autonómica went to their new reserve team.