The church has a square presbytery, with three lancets in the E wall. The transepts are almost completely destroyed, but originally had three square chapels opening off each transept arm. Only part of the S chapel of the N transept survives, showing the remains of groin or rib vaults. The aisled nave had four plain arches on each side at the E end, and a blank wall separated nave and aisles at the W end. Only part of the outer wall of the S aisle remains, and nothing of the N aisle. The W crossing piers were enlarged as a result of a change of design. The abbey was later reduced in size by blocking the transept arches and inserting a new W wall enclosing the two E bays of the nave. A barrel vault was built over the S transept in the later middle ages.

The abbey was founded in 1148 by Toirrdelbach Ua Briain as a daughter house of Mellifont. Domnal Mór Ua Briain became patron after Turlough's death in 1167. The monastery was made subject to Margam in Wales after the conspiracy of Mellifont in 1127. In 1228 the monks fortified the abbey to prevent Stephen of Lexington's visitation. It was suppressed in 1540, but the monks were left in possession until 1579.

The sculpture at Monasternenagh has many parallels with the buildings belonging to the so-called 'School of the West'. The pointed barrel vault and responds of the eastern arch fit a date of c.1170-90, although, like Boyle (Roscommon) the original east windows appear to have been replaced in the first half of the 13thc. by taller lancets. Inconsistencies in the piers of the western crossing arch suggest a change of plan at this point and the plainness of the nave piers makes them difficult to date. The pointed bowtell moulding on the western window suggests a date of c.1210 for the completion of the church.