Timoleague abbey was founded by the franciscan order in 1240 A.D. The abbey was built on the site of a monastic settlement founded by Saint Molaga in the 6th century.

The village's name comes from the Irish for House of Molaga, Tigh Mologa.The abbey was extended by Donal Glas McCarthy in 1312, and by Irish and Norman patrons in the 16th century.

The monks were dispersed by the Reformation, but returned in 1604. In 1612 the abbey was sacked by English soldiers who also smashed all of the stained glass windows, but much of the significant architecture remains. The friars remained in the abbey until 1629.