Today only the cloister at the Mariaplaats remains, behind the Gebouw voor Kunsten en Wetenschappen which houses the Utrecht Conservatory.

Only after an episode in 1133, when Floris the Black entrenched himself in St. Mary's Church during his raids of the diocese, construction was resumed, albeit under a different plan: the nave and the west side were performed in Lombard style, which gave St. Mary's Church a remarkable Italian appearance, unlike anything found north of the Alps.

Unlike the other Romanesque churches in Utrecht, it had two further transepts, was entirely vaulted in stone and additionally had stands above the aisles.

In 1528 the painter Jan van Scorel became canon of St. Mary's Church; among other things he designed a rood screen and some stained glass windows.

After his death he was buried in St. Mary's Church, his tomb becoming the first elaborately decorated grave ever to be given to an artist in the Netherlands.

The church' decline began during the siege of Vredenburg in 1576, when the north tower was destroyed by cannon fire.

After the Reformation, the church was taken in use by the Anglican Communion and the choir was re-purposed to serve as an exhibition space.