The church features several noteworthy stained glass windows, including three by Harry Clarke's studio and a large memorial to Daniel O'Connell.

[4] Most Catholics, including the Capuchins, were expelled from Cork by Murrough O'Brien, 1st Earl of Inchiquin in 1644, but the friary was reopened five years later, in 1649.

[6] O'Leary described the church as "remarkable for its dwarfish dimensions, its utter want of architectural grace, and its perfect seclusion from the public gaze".

[5] The Capuchin and temperance reformer Theobald Mathew arrived in Cork in 1814 and became an active social crusader, working to improve the conditions of the city's poor.

[7] Father Mathew resolved to replace the cramped South Friary with a new church, and a committee was established to oversee the planning.

A competition was held in 1825, and the plan by architect George Richard Pain — who also designed Blackrock Castle and the courthouse on Washington Street — was chosen.

[8] The city authorities offered a site on Sullivan's Quay, facing across the River Lee's south channel to the Grand Parade.

[6] A Pontifical High Mass was held, with admission by ticket, and celebrated by the bishops of Cork, Cloyne and Ross, and Ossory.

[2][25] Two other stained glass windows, likely by the same artist, depict the Virgin Mary and the coat of arms of Pope Leo XIII.

[26] A stained glass window in the east wall, commissioned by the Cork and District Trades and Labour Council and dedicated to Cork Capuchin brother Thomas Dowling, who had mediated an industrial dispute during World War I,[27] was produced by Joshua Clarke to a design by his son Harry Clarke and under his supervision.

Among other figures, it features Christ as Prince of Peace and Saint Francis holding a dove, with the city's skyline at the bottom of the window.

[3][28] Two further windows were commissioned from Harry Clarke and his brother, Walter, depicting the Sacred Heart and the Immaculate Conception being venerated by Munster saints.

Structural flaws and problems such as dry rot evidently riddled the building, to the extent that some suggested demolishing and rebuilding the church from scratch.

[6][37] A plan for a friary which would wrap around the church on three sides was put forward by John Pine Hurley, who "offered his professional services, without remuneration," and the foundation stone was laid during a ceremony on 23 September 1866.

[38][15][39] The current friary, directly adjacent to the church on the west side and designed by Robert Walker in the Venetian Gothic style, was completed in 1884[6] (although some sources say 1888).

[2] Pain was a strong proponent of this style over High Victorian Gothic, which was favoured by his rivals, the Deanes, although he also worked in Classical architecture.

[43] He made extensive use of arched windows, flying buttresses and columns, culminating in a tapering "lacy Gothic spire, seemingly more air than stone.

Patricia Curtin-Kelly's book An Ornament to the City, a survey of Holy Trinity's history, was published at this time with a foreword by the provincial superior.

[49][3] The church features in the novel Beyond Absolution by Cora Harrison,[50] and was used as a filming location in an episode of The Young Offenders television series.