In 1908 the present Altar was erected, the walls were painted with murals, and the stained glass windows were installed. Bishop Sharretti, the Apostolic Delegate, came to bless the completion of the interior decoration of the Church. The organ, from Casavant freres of Quebec, was added in 1919. The exterior of the church was not finished until November 13, 1926, when the two towers were completed. This work was accomplished during the pastorate of Father F. Wafer Doyle, who was Pastor for 18 years, from 1912 to 1930.
By the beginning of the twentieth century the Church of Our Lady was no longer a mission center, but had become instead simply for Catholics in the Guelph area. The many missions which had been founded from Guelph were now established as parishes on their own, and soon the same process would take place within Guelph itself. In 1911 a chapel was opened in a private house on Alice Street, to serve as a mission for the care of Catholics in that part of the city; in due time, in 1924, Sacred Heart Church was built and in 1930 it became the center for an independent parish, the second in Guelph.
By 1931 the time has come for the end of the Jesuit pastoral care of the Church of Our Lady. Over the years the Jesuits had sought to relinquish the parish, and Father Hingston, their Provincial, once more asked Bishop McNally to place it in the hands of the diocesan priests. The Bishop agreed, and on September 6, 1931, Father J. A. O'Reilly, a priest of Hamilton Diocese, became Pastor.
Father Hingston, in a statement read out to the parishioners, explained the reason for the change: the main mission of the Jesuits was missionary or educational work, and since the College once established at the parish had closed long ago and since the parish was no longer a missionary center, it was time for diocesan priests to assume responsibility for the parish while the Jesuits moved on to work more in keeping with their particular call.
Father O'Reilly was pastor for twenty-five years, the longest pastorate in the history of the parish. During his time as pastor two more parishes were separated from the Church of Our Lady to begin their life as distinct communities: St. Joseph's parish, in the western part of the city, in 1952, and Holy Rosary parish, across the river in the eastern part of Guelph, in 1956. The Church of Our Lady parish, which once extended to Lake Huron and Georgian Bay, had now reached its present boundaries.
There were three schools on the grounds of the church: St. Agnes School, built in 1877, St. Stanislaus School, built in 1883, and the Loretto Academy, a High School for girls. Up until 1924 the Loretto Sisters had run a boarding school in the convent, but that was discontinued in 1924 to free space for classrooms for the increasing number of day students. This was followed in 1926 by the construction of the Academy, attached to the convent. On October 10, 1944, Father O'Reilly announced plans to build a Catholic High School for boys. In 1953 the Loretto Academy became co-educational, and in the following year Notre Dame High School was opened at the bottom of the hill.
In 1949 Father O'Reilly encouraged some members of the parish to form Our Lady's Parish (Guelph) Credit Union Limited, within the Ontario Credit Union League. Membership was originally limited to parishioners, and volunteers offered financial services to the members from an office in the basement of the Church on Sunday mornings and Monday evenings. The Credit Union grew rapidly and amalgamated with the Sacred Heart Parish Credit Union. Office staff and a full time manager were hired, and offices were built near the Church on Cork Street. In 1970 the parish Credit Union joined several others in the city to form the Guelph Community Credit Union, and in 1980 a further amalgamation with the Guelph-Wellington South Credit Union formed the Guelph-Wellington Credit Union Limited, which now has three offices in Guelph.
In 1956 Father John Noonan became pastor. St. Bernadette school was established in 1960, St. Paul's in 1964, and Our Lady of Lourdes in 1965. The Loretto Academy and Notre Dame High School were united to form Bishop Macdonell High School in 1962 and an addition was made in 1967 linking the two buildings.
Several changes were made in the property as well. In 1958 a new entrance to the Church from Macdonell Street was constructed and in 1960 landscaping was done on the Northumberland and Dublin Street sides of the property and a new status of Our Lady of the Immaculate Conception was placed on the front of the Church to replace the original one, damaged by weather. In 1967 there was a major renovation of the Church, with a repainting of the whole interior. In 1973, during the pastorate of Father W.L. Ryan, a trust fund was established for the perpetual care and preservation of the Church.