The tower and spire were never finished, leaving the exterior in a state of deliberate-looking plainness, with little ornament beyond the window surrounds and the entrance. Inside, however, the proportions open up considerably, and the church is considered one of the earliest galleried churches in Ireland, a gallery being an upper-level internal balcony running along the walls to increase seating capacity, a feature that became more common in later Protestant church design.

The parish of St. Mary's was carved out in 1697 from St. Michan's, which had until then served the growing north side of the city. Work began on the new church that same year, designed according to Maurice Craig and the Knight of Glin by Thomas Burgh, the architect also responsible for the old library at Trinity College. The interior retains carved box pews and an organ case made by Renatus Harris, an English organ builder of some renown, decorated with figure-sculpture. A preliminary assessment of the crypts in 1998, carried out ahead of redevelopment, uncovered disarticulated human remains and several articulated skeletons alongside fragments of timber coffins. Burials were also found in the narrow strip between the church's south wall and its surrounding railings, the skeletons oriented east-west in the conventional Christian manner. The main burial ground extended further south into the area now known as Wolfe Tone Park, where excavations in 2001 turned up skeletal material alongside post-medieval finds including North Devon gravel-tempered ware, clay pipe fragments, and coffin nails.

The church is on Mary Street in the north inner city, close to the junction with Jervis Street. It has been deconsecrated and repurposed over the years, so it is worth checking access arrangements before visiting. The exterior gives little away, and the unfinished tower means it does not announce itself with any great height. Those with an interest in early post-Reformation ecclesiastical architecture will find the interior proportions and the surviving woodwork worth the detour, and the proximity of Wolfe Tone Park, unremarkable on the surface, carries its own quietly layered past underfoot.