With a growing population in Auckland, the early wooden church was soon found to be too small.

Thus, in January 1846, while in Sydney for the consecration of Father Viard, SM as Coadjutor to Bishop Pompallier, Walter Robertson, architect and surveyor, was commissioned to "design a permanent church for Auckland as a future cathedral" to replace the "temporary wooden chapel".

Two months later, on 1 March 1846, Bishop Viard laid the foundation stone for the new stone church.

Although tenders for drawing scoria, supplying lime and for mason work were called soon after laying the foundation stone, it was not until Robertson's arrival from Sydney in December that construction commenced. Robertson established his business in the Shamrock Cottage, Albert Street, around the corner from the St. Patrick's site.

Fifteen months later, on 19 March 1848, the stone church was solemnly blessed and opened by Bishop Viard. The cost of the building was £1387.

Later the same year, on 20 June, the stone church was consecrated as the Cathedral church of the Diocese of Auckland - New Zealand's first cathedral church.