The first Catholics in Waukee were probably of Irish descent, coming as crews working on the railroad. Before the coming of the railroads, it is reported in other histories that the Catholic people would take their wagons or ride the stage into Des Moines once a year to make their Easter duty, since Des Moines had the nearest Catholic church. Ethel Forret recalled when a priest came to Waukee and a Mass was said at the home of Patrick Hogan, the section boss of the Des Moines Valley Railroad. It is doubtful that a priest came once a week; most likely it was once a month. Some of the names from the 1870 Waukee census that we know were Catholics of the time are: Broderick, Finnane, Forret, Lauterbach, Hogan, Wacht, Feller and Manders.

The first Catholic Church was erected in Waukee about 1880. The church was a frame building seating about fifty people and was built under the guidance of Father Burke, who then lived in Dallas Center. The parish was conducted as a mission from Dallas Center and, for a time, from Granger. In 1912, Bishop Davis of Davenport sent Father Francis Larkin to be the first resident pastor in Waukee. Father Larkin built the rectory on a lot north of the church. In 1917, Father Daniel Sheehy was appointed pastor of St. Boniface, which then included mission churches at Adel and Dallas Center.

The growth of the parish was such that in 1918, the parishioners, along with their pastor, decided to erect a larger church. With permission from Bishop Austin Dowling, a building committee was formed. Lay members of this committee were John Hanlon, Sr., Joe Forret, Andrew Weil and Nick Forret. Fifty self-sacrificing and generous families donated $15,185 to the building fund in 1918. The substantial and devotional church located at 250 4th Street in Waukee was built for $18,000 and holds nearly 200 people. Among the beautiful stained glass windows is a very ornate work of art representing “Our Savior on Calvary,” which dominates the north wall over the main altar (and which is now in the chapel of the current facility).

The opening of a coal mine near Waukee two years later in 1920 brought an additional twenty families of Italian descent into the parish. Father William Coughlin served as pastor from 1921 to 1936. He was succeeded in 1936 by Father M. D. O’Neil. After this, Father Declan Dower served as pastor for two years and Father William. J. Devine for one year. Father John Aldera was pastor from 1945 to 1953. In 1947, during his pastorate, the lot west of the church at 250 4th Street was purchased and the parish hall was constructed. Complete with kitchen facilities and fixtures, it serves the community well for parish and public activities. Its most important function is as an education facility, where preschool and school age children still gather for Sunday School and Religious Education.

Father Maurice Schulte served as pastor from 1953 until 1964. In 1964, Father John Clarke was appointed pastor. Father Thomas Pfeffer succeeded Father Clarke in August 1979. During his time as pastor, programs and improvements were undertaken to involve and serve the increasing number of parishioners. To help with the growing needs of St. Boniface and St. John’s in Adel (which was at the time served by the same pastor and parish office), Sister Barbara Marshall, a Sister of Christian Community, was hired in August 1981 as Pastoral Minister. As the parish grew, St. Boniface hired its own Pastoral Minister in August 1983, Sister Bernadette Engelhaupt of the School Sisters of St. Francis. Sister Theresa Engel of the School Sisters of St. Francis succeeded her in August 1991 and stayed until July 2002.

Father Anthony Aiello was appointed pastor in July 1985. In 1992 Bishop Bullock decided that St. Boniface and St. John’s in Adel should each have their own resident pastor. Father Bob Schoemann was appointed pastor in July 1992 to a St. Boniface parish of 297 families. The parish was still growing. In 1994, a parish self study was done to assess how to meet the needs of this rapidly growing parish. Through a combination of purchase and gift from Phil and Charlotte Broderick, the parish has 13.26 acres located at the southwest corner of University Avenue and Warrior Lane in Waukee.

In the fall of 1998 a capital campaign called “Celebrating the Past…Building for the Future” was initiated and over $1,143,000 was pledged toward the building of a new facility. The new facility at 1200 Warrior Lane was opened on January 27, 2001, with the Consecration of the Altar and first Mass.

This new facility contains a temporary worship space (which will ultimately become a parish hall), a gathering space and parish offices (except for religious education offices, which remain at the parish hall). Future construction phases will consist of a permanent church and religious education classrooms. The existing parish hall at 250 4th Street will continue to be used until no longer needed for dinners and religious education classrooms.

In July 2002, Father Vince Rosonke was welcomed to St. Boniface by over 630 registered families.  In October 2006, with over 850 families in the parish, the pledge drive for phase II was initiated.  Over $1,950,000 was pledged toward "Building Faith".  These pledges, along with monies from the sale of the generous gift of land from long-time parishioner Mabel Loschen, enabled Phase II to move forward.  It was also Mabel's gift which allowed the parish to remove and re-install the beautiful stained glass windows from the 1918 church.  Phase II of the building project, which included the new sanctuary, faith formation center, parish hall and permanent offices, opened in the fall and winter of 2007.  Staff moved to the new office area, that accommodates seven senior members and four support staff, in May 2007.  The faith formation center was dedicated in September 2007.  It contains 24 classrooms and a 75 seat all-purpose room, the "Mary & Joseph Room".  The new sanctuary was dedicated on December 8, 2007.  This new sanctuary seats 1,000 people.  Phase II ended with the completion of the new parish hall and kitchen facilities in January 2008.

The parish continues to grow at a rapid rate. At the start of 2015, the parish had over 1500 familes. Faith formation grew from 938 students in 2010 to 1171 in 2014.