St. Joseph Baptist Association was organized at Bethel Church in Andrew County in 1872 after a preliminary meeting had been held at Easton in 1871. Sixteen churches composed the association from the beginning. We could not find a list of those churches. According to the Annual Report of 1884, of which we have a copy, the following 25 churches composed the association: Bethel, Bethlehem, Contrary Lake, DeKalb, Frazer, Flag Springs, First St. Joseph, High Prairie, Lafayette, Mount Pleasant, Mount Vernon, Maysville, Missouri Valley, New Hope, New Harmony, New Prospect, Nodaway Missionary, Sugar Creek, Savannah, Taos, Whitesville, Walnut Grove, South St. Joseph, Fontainbleau, and King City. These last two churches were received into membership during the meeting. By 1887, thirty churches were a part of the association and in 1927, forty-one churches were reported. 

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According to the constitution printed in the 1884 Annual, "The Association shall at each Annual Meeting, appoint an Executive Board, whose duty it shall be to employ one or more Missionaries (according to the funds contributed by the churches) to labor in destitute places within the bounds of the Association, in preaching the Gospel and supplying the people with religious and denominational books." The first such missionary who we found record of, in the 1884 Annual, was Bro. B.F. Rice who started his work on November 15, 1883. Many more missionaries were employed over the following years. During the Annual meeting in September 1906, the decision was made to hire one, "first class, high grade man to take charge of and oversee the associational work for more than one year at a time." The Executive Board created the office of Secretary of Missions and called Rev. J. P. Jenkins who started on December 1, 1906. He published the first association paper, titled The St. Joseph Baptist Record in April 1907, which listed the "doings" of Baptists throughout the association. He did this in response to the general feeling that there was a disconnect among the people in not knowing what other churches were doing. District Missionary for the Association became the new title and for the next several years that title changed with the following missionaries being called to fill the position when it became vacant: Bro. W.O. Dixon, Bro. W. A Pipkin, Rev. A.J. Umberger, Rev. C.C. Cunningham, Rev. D.H. Howerton, Rev. W.D. Baker, and Dr. Wm. H. Butler. 

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In April of 1917 the Associational Executive Board appointed a committee to formulate plans for the incorporation of the Association. This was accomplished and in 1919 the association received their Articles of Incorporation. 

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On September 1, 1945 Lee Lewis became the Associational Superintendent of Missions. He was succeeded by O.R. Burnham, and D.B. Hoskins. The association bought and furnished the old Wyatt Park Parsonage as a home for the Superintendent of Missions. Rev. Cecil H. Franks became the next superintendent and an office was set up for the Superintendent of Missions in the Savannah Avenue Church building. In 1959 the constitution was amended to add the Superintendent of Missions as an ex- officio member of the Executive Board. Dr. Clayborn E. Landers became the new Superintendent of St. Joseph Baptist Association in 1959. He suggested relocating the associational office and hire a full-time secretary. The new office was located downtown at 1029 Frederick Ave and a new electric sign was erected on top of the office. When he resigned in 1963, Rev. Robert Eberting Jr. was called as Interim Superintendent, then on February 3, 1964 he was called as the new Superintendent of Missions. The lease expired on the office space for the association so the office was moved to 4705 B Frederick Blvd. It was decided that the association should look into plans for a more permanent facility. 

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Rev. Eberting recommended the association sponsor a BSU starting in the fall of 1965. During the 1967 Annual Meeting, the decision was made to set aside $10,000 toward acquiring land and constructing an adequate building for an associational office. During the Associational Executive Board Meeting on January 11, 1968, the board voted to request the Missouri Baptist Convention to assume responsibility for Student Work at Missouri Western College in consultation with associational leaders. On July 2, 1968 the Executive Board voted to offer a gift of $10,000 (monies that had been set aside) to the Executive Board of the Missouri Baptist Convention and request the convention to purchase, for student work, a 3 acre tract with a new house at 4414 Mitchell, adjacent to the new campus of Missouri Western College. On July 9, 1968 the Executive Board of Missouri voted to accept the gift of our association and purchase for $45,000, the property for student work and that negotiations be made with SJBA as to the use of the building until such time as the Executive Board could establish the student work. February 1, 1969 the Associational Office moved into the building at 4414 Mitchell and the facilities were shared with the Baptist Student Work. 

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During the 1973 Annual Meeting, 516 people registered with 35 of 37 churches being represented. A new organizational chart was proposed with purposes and descriptions explained for each organization/position. This was adopted in 1974. Upon the resignation of Rev. Eberting, Rev. John C Burnham was called as the new Superintendent of Missions. This title changed in 1975 to Director of Associational Missions. On April 25, 1979 the MBC submitted a request for full use of the present BSU building. The Association Building Committee proposed to the MBC that since we have a strong desire to stay within the vicinity of the BSU, that the state deed one half of the land to the association for the purpose of building a new associational office. The MBC Board gave approval in 1981 for the conveyance of a tract of land to the association upon the condition that it will be the association's responsibility to relocate the driveway and construct a hard surfaced parking lot with sidewalks and steps if necessary. 

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During 1980 it was recommended to have the April Board meeting become a semi-annual meeting of the association and that two part-time secretaries be employed. The Senior Adult Committee was also created. 

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Ron Wynne became the new MBC full-time BSU Director on August 15, 1981. The new (current) Associational building and parking lot was completed and the BSU occupied all of the present building. December 13, 1981 the current Associational Office was dedicated. Rev. John Burnham retired on July 31, 1991 and Rev. Charles Sexton was called as the new Director of Missions. The Association received certification as an authorized Seminary Extension Center in January 1992. Rev. Sexton retired September 1, 1995 and Dr. Clyde R. Elder was called as Director of Missions starting April 7, 1996. 

In 2001 the Association organized a Disaster Relief Team to be part of MBC and SBC Disaster Relief efforts. A block party ministry was started with the purchase of a Block Party Trailer and outfitted with food machines, bounce houses, and games. An eight passenger van was purchased for associational ministry use in 2004. In July 2005, the Association called Paul Damery as the Full-time BSU Director. A garage was built next to the associational office in 2007, for much needed storage and to house the van. March 31, 2009 a Reorganizational Structure for the association was adopted on a trial basis and was adopted as official in 2012. October 15, 2015 Dr. Clyde Elder passed away unexpectedly. Pastor Allan Lane became the Associational Acting Coordinator. The associational office basement was repaired and remodeled and new flooring installed upstairs. 

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Brother Roger Brumley was called as the new Director of Missions starting on June 18, 2017. Over the course of the next few years, the association purchased a new 15 passenger ministry van and added more equipment to our two Disaster Relief Trailers. In 2019, the BSU changed it's name to Christian Challenge. In May of 2024, Paul Damery resigned from his position as the Christian Challenge Director. Brother Roger Brumley resigned from the Director of Missions position in August of 2024. Isaac Whitman was called as the new Christian Challenge Director in August 2024. As of 2024, the Association consists of 43 partnering churches.