The parish was originally established as St. Kunigunda’s in 1855 in the Diocese of Dubuque. The parish was named for St Kunigunda of Slavonia, and served the German immigrants who settled in the western part of the city. Judge C. G. R. Mitchell donated the property for the church. A stone church building was dedicated May 25, 1856 by the parish’s pastor Father Flammang, who conducted the services in Latin and German. He was succeeded in 1857 by Rev. John Baumgarten who stayed for a year, and then the parish was without a pastor for six months. Rt. Rev. Msgr. Niermann became pastor on April 2, 1859.
As the parish continued to grow it was decided to build a new church. The cornerstone was laid in 1881, the same year as the Diocese of Davenport was established. It was at this time that the parish name was changed to St. Joseph, probably because if its proximity to St. Mary’s Church which was built two blocks to the west in 1867. The new church was dedicated on September 16, 1883. The building is a rectangular plan Gothic Revival structure with decorative brickwork and a central entrance tower. The former church building was converted into a school. St. Joseph School was served by the School Sisters of St. Francis from Milwaukee.
Significant changes occurred starting in the 1960s. The ethnic makeup of the neighborhood around St. Joseph changed. The original German immigrant community was gone and the people who replaced them were largely not Catholic. Changes were made in the liturgy to accommodate the reforms of the Second Vatican Council. The liturgies were now celebrated in English. The communion rail was removed and a new altar, which allowed the priest to face the congregation, was put in place. The old altars and statues, however, remained in the church. By the 1970s sizeable numbers of Mexican Americans began moving into the area, and a liturgy in Spanish was added. The Spanish speaking community stayed until the late 1980s, when they moved to St. Mary’s.
The school continued until 1968 when it was merged with St. Mary’s School and renamed Holy Trinity. The merger lasted into the 1990s when St. Mary’s ended its participation. Because of declining numbers the diocese decided to close the school in 1999. An independent group of people bought the school that year and it reopened as Holy Trinity Mission School. A few years later it was renamed Marquette Academy.
The parish, which never had defined territorial boundaries because it was established as a German ethnic parish, continued to decline in numbers and it was also closed in 1999. The building became a part of Holy Trinity Mission School. In 2008 the church and rectory were purchased by a non-denominational congregation and it became Legacy Church.