In 1892 Father Cleary was invited by Archbishop John Ireland to come to the diocese of St. Paul. Resigning his Kenosha pastorate, he came to Minneapolis and during the fall and winter conducted meetings in public halls in the south part of the city on the doctrines of the Catholic faith. He soon became known as "The Public Hall Apostolate" and became exceedingly popular in Minneapolis. Father Cleary realized a need for a church to serve the people in the area south of the business district, and he organized and built the old St. Charles Church at 4th Street and 13th Avenue. The church was erected in 1894 and for 17 years Father Cleary was its pastor. His foresight told him that another new church would be needed in south Minneapolis and in 1909 after St. Charles Church burned and upon appointment by Archbishop Ireland, Father Cleary commenced the labors that brought into being The Church of the Incarnation.

Early problems were abundant for Father Cleary. These included organization of the community, purchase of a land site for the new church and school, and the locating of a temporary facility which could serve as church in the interim. Organizing the church was undoubtedly the easiest of the three major problems for not only were the people in the area eager to have a church, but also many members of the St. Charles Church were eager to join Father Cleary's new church. To insure the possibility of taking out mortgages, a corporation was formed with Archbishop Ireland as president, Father James Cleary as vice president, Mr. Peter Carter as secretary, and Thomas E. Sands as treasurer. The Scribner- Kelly Land Company of Minneapolis donated a section of land on the corner of 38th and Pleasant Avenue for the erection of the church. To make the deed transaction legal, Father Cleary purchased the land for one dollar and signed the deed on September 17, 1909. The site for Incarnation at that time was a cornfield and the area around the church was so sparsely populated that the new church received the nickname "Cathedral of the Cornfields. "

Father Cleary was able to obtain the use of the Ark Lodge, a public hall, and the first mass celebration was on October 3, 1909. About 200 families attended the services. For 18 months the Ark Lodge was the home for the Incarnation Community until the new facility could be built.

It was agreed to by Father Cleary and the parishioners that the new facility would serve a dual purpose. In most of Father Cleary's previous parishes a catholic school had always been a high priority. He believed that religion and education went hand in hand and that both made up the strength and growth of any community. Money was definitely needed for the construction of the composite church and school building. One of the first fundraisers held was a bazaar in an abandoned skating rink on the corner of Lake Street and First Avenue South. The net results were $6,101.00, considered a large sum. Father Cleary also requested the assistance of the men of the parish in a pledge drive to help raise funds for the construction of, the new facility.  

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During the winter of 1910 ground was broken for the first building; the cornerstone was laid by Archbishop Ireland on September 4, 1911. The building was a substantial two story brick structure and was called the "Institute of the Incarnation" (Cleary Hall). On the first floor was an auditorium and temporary church with a seating capacity of 800. On the second floor were 6 classrooms.

Father Cleary called on his old friends, the Sinsinawa Dominicans from the congregation of the Most Holy Rosary to open the school which had 160 pupils. This was on the 4th of September 1911. Sister Mary Raymunda, Superior, Sister Mary Antonia, Sister Mary Clarice and Sister Mary Columkille opened the school and started a relationship with the people of Incarnation which would last many years. At first only pupils in the first six grades were admitted so the first group to graduate was the class of 1914, which had 19 students. To accommodate the new sisters a wooden frame house was converted into a convent. This is the present site of Moynihan Hall.

Father Cleary and his two assistants, Reverend George Carroll and Reverend Waiter Daly were also in need of a residence. Construction for the new rectory began in March of 1912 and was completed in October of that same year, at a cost of $20,814.00. The parish rectory was constructed as a three story building containing 16 large rooms and a large basement. In later years a three-car garage was also added.

The small parish began to grow immediately and with its famous founder, Father Cleary, at the head, it was not unusual to see real estate ads which read, "Lots for sale in Fr. Cleary's parish". One of the first major celebrations in the parish was Father Cleary's forty-first anniversary in the priesthood, on March 25, 1913. The mayor of Minneapolis presided and among the speakers were: the governor of Minnesota, president of the University of Minnesota, and Father Cleary's close friend, Archbishop John Ireland.

In May of 1916 a meeting took place between Father Cleary and many of the parishioners to begin the planning of a single church structure. A committee was established consisting of: T.E. Sands, Peter Carter, J.W. Moynihan, J.D. Coleman, J.C. Whelan, J.J. Quinn, Henry Reilly, and J.C. Donahue. The committee set a goal of raising funds of $100,000.00 to construct the new facility. Construction began with the groundbreaking ceremony on October 10, 1916. Father Cleary turned the first spade full of dirt and declared the site to be the first Catholic church in South Minneapolis.

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