St. Boniface Parish was founded by German immigrants in 1862, making it one of the older parishes in the City of Chicago. After the church escaped the Great Chicago Fire of 1871, it became a refuge for the many people left homeless. The area around the church quickly developed in the aftermath of the fire. Construction of a new church several blocks away began in late 1901, with the cornerstone of the church laid in September of 1902. Designed by Henry J. Schlacks, the Romanesque structure was dedicated on June 5th, 1904.
As the 1910's came to an end, the German immigrants moved to other parts of the city, and Polish residents settled in the area. Cultural differences resulted in a decline in membership, but new leaders worked to bridge the gap between the two communities, and the parish recovered. By the 1950's much of the area was settled by Puerto Ricans, and the church became the first in the area to offer Spanish sermons.
Like many churches around the city, St. Boniface lost members through the 1970's. The parish school closed in 1983 due financial hardship and low enrollment. In June of 1990, the Archdiocese of Chicago announced plans to close 28 churches across the city, including St. Boniface.
Through the 1990's and 2000's, most of the buildings around St. Boniface are demolished, starting with the convent in 1994, followed by the school in 2003 and the rectory in 2011. The church narrowly avoided demolition in 1999 thanks to the efforts of preservation groups, and plans for redevelopment begin to circulate. At one point in 2006 a local Coptic Church expressed an interest in buying and renovating the church, but was rejected in 2008. The church once again escapes demolition in early 2009, and was instead sold to a developer.
In the years since, numerous plans to either redevelop or demolish the church have come and gone. Recently another demolition permit was issued, but plans to convert the church into a performing arts school are moving forward. On July 24th, 2016, The Chicago Academy of Music announced that it was "98 percent of the way" to taking over the church and preventing demolition.