By 1870 the original church had become incapable of accommodating the increasing congregation as well as being dilapidated and insecure so a new and larger building was needed.
The Church Chronicle of 15th November 1887 describes the acquisition of the present site: "For the splendid site on which St Mary's is built, we are indebted to the former incumbent, the Rev R Moffatt. The piece of land originally granted by the Crown for Church of England purposes on Kangaroo Point was that on which Mr. Barker's house now stands and extended from Main St. to the river - a most unsuitable and in fact utterly useless piece for the object for which the grant was made. Accordingly, Mr. Moffatt who was then Parliamentary librarian as well as incumbent at St Marys, made good use of the influence which his position gave him among those in authority and succeeded in effecting an exchange of one half of the original Crown grant for the magnificent site on which there stands now our Church and Sunday School and where it is hoped a Parsonage will soon be seen".
Rector Rev David Court in 1870 persuaded the Parish to embark on the task of building a new permanent Church on the recently acquired site and architect Mr. Richard Suter was engaged for design and construction.
An initial contract was let to Alfred Grant builder, for construction of the nave as far as the current porch, and this was later extended to include the chancel after a construction interruption, while the parish resources struggled with the significant financial burden the new building represented. The other portion of land granted by the Crown was sold in 1872 to help fund the new building.
This photo (above) shows the church as completed in 1873 with the stumps of recently felled trees in the foreground. The plan was a simple open rectangle with a semi-circular apse area. The current "temporary" vestry was attached adjacent to the apse. External stone walling has provision for construction of a permanent vestry to the left of the entrance porch above, where toothed (keyed) stone bonding points have been included.
On 29th April 1872 the Marquis of Normanby, Governor of the colony of Queensland, laid the foundation stone, and the first Bishop of Brisbane, Bishop Edward Tufnell, consecrated the completed building on 5th November 1873.
The main structure of St. Mary's is formed of roughly dressed, coursed random rubble stone, mostly Brisbane "tuff". The walls carry a traditional timber truss roof frame, steeply pitched, with stone buttresses on the external walls to support the roof loadings. The diagonally planked timber ceiling lining provides essential bracing to the roof structure, as well as a subtle visual contribution to the traditional atmosphere evoked by the heavy timber trusses. The original roof was of ironbark shingles, replaced by galvanized iron around 1921. Internally there are dressed softwood timber flooring and timber plank pews. Some of the pews still carry evidence of youthful "doodling" over the years, reflecting the proximity of a school on adjacent land.
In 1892, nine years after completion, the Church was damaged during a cyclone. The whole western end roof was lifted bodily and thrown into the nave (see image below). During a year of reconstruction the church was enlarged by addition of a two bay transcept, the roof repaired, a different belfry built, and a subtle increase in floor to ceiling height in the nave was accomplished. Due to the efforts of Bishop Webber, the parish and the wider community St. Mary's opened on 25th February 1893 free of debt.
During February 1893, the greatest flood on record inundated Brisbane. The Church Chronicle of April 1893 mentions that the rededication had to be delayed several times and that the hall served as a refuge while the flood waters prevailed.