Above the Altar hangs the Crucifix which was designed by the architects for the 2005 restoration of the Cathedral and was made in the same studio in Madrid as the Tabernacle. The design of the Crucifix is reflected in the panel above the main doors to the Blessed Sacrament Chapel.
The Sanctuary is flanked on the north side by the Blessed Sacrament Chapel. The Tabernacle was made in Madrid and rests on a plinth of the same limestone used for the Altar. The chapel is enclosed within decorative railings made by Lavell's in Belfast.
At the entrance of the Blessed Sacrament Chapel hangs the silver sanctuary lamp, an intricate piece of late Celtic Revival work by Eagan's of Cork. This was presented in the 1920's by the McGowan family, who were members of St Peter's Parish.
On the south side of the sanctuary is "The Lady Chapel". It contains a copy of a 15th century statue of the Madonna and Child. The original of this statue is in a Cistercian Abbey in Normandy in France. It was St Malachy, the patron of this diocese, in his friendship with St Bernard of Clairvaux, who introduced the Cistercian Order into Ireland.
In the centre of the apse wall is the Bishop's Chair, or Cathedra. This is the symbol of the unity of the Diocese under the pastoral care of the Bishop and it is from the word Cathedral come from this. This "Chair" in St Peter's was first used by Bishop Patrick Dorrian, who was Bishop of Down and Connor from 1865 - 1885.
The Altar and the Ambo are both of limestone and were carved by Ken Thompson of Cork. The front of the Altar depicts Christ with the Apostles at the Last Supper, but unusually the artist has Christ with pierced hands in anticipation if the crucifixion. To mark the dedication of this Altar and the reopening of the Cathedral after restoration on 6th February 2005 a chalice was presented on behalf of Pope John Paul II as a sign of his pastoral affection and unity with the Diocese of Down and Connor. The floor of the sanctuary is of artistic mosaic created by Sergio Bendetti.
There are two side chapels in the Cathedral: on the north side is the Chapel of Resurrection where a former bishop, Dr William Philbin, was buried in 1991. The window depicts the early Easter morning encounter between the risen Christ and Mary of Magdala. It is the work of the Irish artist Roisin Murphy-O'Dowd, and it is her last work, as she died shortly after the completion of this window.
On the south side of the Cathedral is the Chapel of Reconciliation, with the Evangeliarium which contains the Book of the Gospels. It is also the chapel that the Sacrament of Penance and Reconciliation is celebrated.
The Aumbry displays the Holy Oils used for the administration of the Sacraments and the Dedication of new Churches and Altars. The Holy Oils are blessed by the Bishop on Holy Thursday morning at the Mass of the Chrism. The Aumbry was erected in memory of Father Hugh Mullan and Father Noel Fitzpatrick who were killed while anointing those wonded on the streets of Belfast in 1971 and 1972 respectively during civil unrest.
Near the Narthex is the Baptismal Font also by the artist Ken Thompson. It is located near the entrance to the Cathedral to represent the fact that it is the Sacrament of Baptism by which Christians enter the life of the Church. The shape of the Baptismal Font follows the ancient custom of being octagonal to remind us that it was on the "eighth" day that Christ rose from the dead. The font is adorned with geometric carvings and portrays the Baptism of Christ in the river Jordan. On the top are inscribed in Latin the words of St Paul "Unus Dominus, una fide, unum baptism", There is one Lord, one Faith, one Baptism (Eph 4:5).
Above the organ gallery is the west window which has a central panel showing Christ conferring the keys of St Peter, (Mt 16:17-19). On either side there are depictions of St Patrick and St Malachy, the National and Diocesan Patrons. Other panels show the holy Spirit and the heraldic arms of the Diocese and also of Pope Benedict XV (1914-1922). The side panels depict emblems of the Passion and a Monstrance with the Blessed Sacrament, appropriate for a Cathedral with perpetual adoration.