Since the seventeenth century, the majority Catholic population of Ireland had lived under the rigours of the Penal Laws, a series of enactments which were designed, in the words of the Anglo-Irish historian Lecky, "to deprive Catholics of all civil life; to reduce them to a condition of extreme, brutal ignorance; and, to disassociate them from the soil".

The architect James Joseph McCarthy, a self-styled "pupil" of Pugin, was appointed to oversee the completion of the cathedral.

The position as architect to the new cathedral was rather a difficult one for, by the time of McCarthy's appointment, the walls of Duff's Perpendicular building were already 10 metres (34 ft) high and had reached the top of the aisles.

Dixon died in 1866 again before the completion of the cathedral and once again the project was abandoned under his elderly successor Archbishop Michael Kieran.

Archbishop McGettigan commissioned painted murals to adorn the walls of the Lady Chapel and stencilling was applied to its ceiling.

In 1879, the seven-light east window was filled with stained glass by Earley & Powell of Dublin and work began on the seven terrace flight of steps to the plaza in front of the west end.

A fundraising bazaar was organised in 1900 and the firm of the architect William Hague of Dublin (who had inherited much of McCarthy's practice on the latter's death) was appointed to make plans.

The bazaar raised over £30,000 and Logue travelled to Italy with his architect to visit marble quarries and artisan workshops, choosing materials and craftspeople to carry out Hague's plans.

Ashlin designed a High Altar carved from Carrara marble, Lapis Lazuli and Jasper to sit before Hague's rood screen and the Italian sculptor, Cesare Aureli was commissioned to carve a frontal in alto relievo of Leonardo da Vinci's Last Supper.

The Cathedra throne projected in three divisions at the second bay on the North side with canopied niches, having crockets and pinnacles and surmounted by a marble spire.

The canopy of the pulpit, rising to a height of nearly 36 ft. was carved in Austrian oak painted white and inlaid with coloured enamels and gold leaf.

The antependium contained three bas-relief groups, the work of the eminent Roman sculptor Michele Trepisciano (1860–1913) showing "The Presentation of the Blessed Virgin in the Temple", "The Assumption" and "The Coronation of the Virgin" recessed in separate panels with cusped heads, and columns of Breccia di Seravezza antica and Breccia Corallina marbles.

The tabernacle, inlaid with Corsican Jasper, was in the form of a cube topped with a roof of fish scale carvings and finished with two large statuary marble standing angels.

William, Cardinal Conway was appointed to the See of Armagh in 1963 although he had been serving as leading Irish participant in the Second Vatican Council since its inauguration.

The reforms on liturgy required greater congregational participation in Catholic services and for some time it had been felt that the 1904 marble works at the crossing had impeded large-scale ritual in the cathedral.

The pulpit was dismantled and broken up and the side altars to Saints Brigid and St Joseph were removed and relocated in other churches.

To replace the rood cross, a huge sculpture entitled "The Tree of Life" was commissioned from Imogen Stuart, the German-born Irish sculptor.

"Neither the quality of the replacements nor the skill of the craftsmanship can disguise the total alienation of the new work from the spirit and meaning that was McCarthy's ecclesiological and architectural inspiration.

Architectural historian Jeanne Sheehy wrote of the re-ordering as "the replacement ... of a fine late Gothic revival chancel with chunks of granite and a tabernacle that looks like a microwave".

Although the decorative style of the cathedral was thus significantly changed in 1982, the building itself had not undergone any major structural works since the replacement of the aisle roofs in 1904.

As a result of the construction methods of the walls and wear to the roof, damp had damaged much of the mosaic and the painted decorations had been dulled with smoke and dust.

A Diocesan committee charged with overseeing these major structural works to secure the building decided that the time was also ripe for reviewing the much criticised sanctuary.

The altar was inspired by early-Irish crosses and has imagery of Christ (Crucified, Risen, Return in Glory), flanked by Apostles, on three sides.

The fourth side visible from the main body of the Church shows Our Lord with four Irish saints: St. Patrick, St. Malachy, St. Brigid and St. Oliver Plunkett.

Two pairs of brass gates which had survived from the 1899 marble Rood Screen were replicated several times over, welded together, topped with newly-designed Gothic cresting and made into a new fully brass screen behind the high altar, restoring a separate Lady Chapel area as the culmination of an ambulatory around the sanctuary area.

The rebuild was designed by the late John Holmes with the cathedral organist Baron George Minne as a consultant.

Positif: Gelind Gedeckt 8, Bell Gamba 8, Singend Principal 4, Koppelflute 4, Nasard 2 2/3, Octavin 2, Tierce 1 3/5, Petit Cymbale III, Cromorne 8, Zymbalstern, Tremulant (adjustable), Octave, Great to Positif, Swell to Positif, Bombarde to Positif, Great: Double Diapason 16, Open Diapason 8, Gamba 8, Bourdon 8, Principal 4, Flute Ouverte 4, Twelfth 2 2/3, Fifteenth 2, Fourniture V, Cymbale II (an overall crazy screaming affair,) Bombarde 16, Trompette 8, Clairon 4, Swell to Great, Positif to Great, Positif Sub-Octave to Great, Swell: Open Diapason 8, Stopped Diapason 8, Salicional 8, Unda Maris 8, Principal 4, Doublette 2, Plein Jeu III, Basson 16, Cornopean 8, Clarion 4, Tremulant (adjustable), Octave, Sub-Octave, Bombarde: Flute Harmonique 8, Voce Umana 8+8, Carillon III, Orlos 8, Trompeta Magna 16 (TC from Trompeta Réal 8), Trompeta Réal 8, Clarin 4 (From Trompeta Réal 8), Campanabella (one octave of bells), Pedal Gravissima 32, Principal 16, Violonbasse 16, Bourdon 16, Double Diapason (Great) Violone 8 (From Violonbasse 16), Gedecktbass 8, Principal 4, Doublette 2, Grosse Fourniture III, Carillon II, Bombarde 16, Basson 16 (Swell) Trumpet 8 (from Bombarde 16), Clarion 4 (From Bombarde 16), Orlos 4 (From Orlos 8, Bombarde) Positif to Pedal, Great to Pedal, Swell to Pedal, Bombarde to Pedal, Great and Pedal Pistons Coupled.