An agreement between the National General Assembly of the Presbyterian Church and the Congregational Associations of New England, the 1801 Plan of Union, allowed for mutual support between denominations and spurred a joint effort in evangelizing the American Frontier. The Plan of Union also enabled churches of either denomination to hire ministers from the other. From 1826 to 1833, the American Home Missionary Society sent 24 missionaries of both cooperating denominations to Illinois. Although many of these missionaries were from New England, a stronghold of Congregationalism, the very first churches they established in Illinois were Presbyterian. A large percentage of settlers in Illinois during this period were land-buying colonists from the Northeast, who brought with them their Congregational beliefs and traditions. These Congregational roots along with the fervor of several Congregational ministers and missionaries from the Home American Missionary Society resulted in the creation of the first Congregational churches in Illinois in 1833. By 1834, a group of about 30 churches in the central western area of Illinois had established the first Congregational Association. This first group, the Congregational Association of Illinois was renamed the Quincy Association in 1864. The Quincy Association absorbed the Western Illinois Christian Conference, formed in 1931 .

In 1835, an assembly of 18 churches created the Fox River Association at a convention in Big Grove. Next, the Rock River Association was formed in 1838 in the Rock River Valley. The Rock River Association was marked by a high concentration of fervent abolitionist pastors, many of which were tried for harboring slaves. Another distinguishing trait of the Rock River Association was a large percentage of pastors from New England who identified as Oberlin Perfectionists. The theology of Oberlin Perfectionism stemmed from the teachings of Charles G. Finney and emphasized a belief in a second stage of Christian life characterized by a perfect trust in God and complete commitment to his way. The American Home Missionary Society refused to fund associations heavily populated by Oberlin believers and Congregationalists in Illinois were similarly uncomfortable with this new school of thought, which many believed broke from Congregational doctrine. The political activities of abolitionists and the tensions surrounding Oberlin believers led to the dissolution of the Fox River Association in 1848. These first three Congregational strongholds in Illinois lacked statewide connections and the New England Congregational Associations were not yet convinced of the strength or doctrinal purity of these western Congregational Associations. Also, the Presbyterian Assembly, which had abrogated the Plan of Union in 1831, also felt that they could encroach on the regions Congregational missionaries were cultivating. The Presbyterian denouncement of the Plan of Union was triggered by the strict abolitionist stance of Congregationalists, as well as anger towards the provisions in the Plan of Union that allowed mixed denomination churches to be governed by Congregational committeemen instead of Presbyterian elders. Presbyterians were also uncomfortable with the admittance of Congregational committeemen into the General Assembly and the lack of adherence to Presbyterian doctrine in mixed churches. In an effort to create a strong, unified body of legitimate Congregationalists to present to the Presbyterians and Easterners, the Congregational Conference of Illinois was formed in 1844. During the Conference’s first official convention, resolutions strongly condemning slavery were adopted.

In 1844 the Central Association was formed from churches that spanned a huge territory stretching across the state. From this original association, the Bureau, Central West, and Central East Associations were later formed. However, a smaller Central Association survived until merging with the Central Christian Conference in 1931 to form the Central Congregational Christian Association. In 1848 the Rockford Association was formed from a portion of the churches originally affiliated with the Rock River Association. Likewise, the Geneseo Association was created in 1851 from the churches that broke off from the southern portion of the disbanded Rock River Association. Rapid population growth took place in Illinois from 1850 to 1860 and resulted in the formation of several new Congregational associations. The population growth stemmed from several developments. First, Chicago became known as the commercial metropolis of the Midwest soon after the Illinois Michigan Canal was created in 1848. Also, the introduction of railroads into Illinois led to a fresh wave of New England Congregationalist setters in the Northern and Central regions of the state. Formed during this period in 1852, the Elgin Association resulted from the assembly of 16 of the original 45 churches that constituted the Fox River Association. Also established during this period of population growth was the Morgan Association, founded in 1851 and renamed the Southern Association in 1858. The Bureau Association came into being in 1857 after several churches broke off from the Central Association. Similarly, in 1860 the Central West and Central East Associations were formed from the merger of new churches and churches originally attached to the Central Association. The Central East Association also integrated a number of churches that detached from the Chicago Congregational Association.

Before and during the years of the Civil War, Congregationalism was the only major denomination located exclusively above Mason Dixon line. Due to this placement, Congregationalists generally did not experience slavery among their settlements or depend upon slavery for their financial stability. Congregationalists, with their beliefs regarding equality and ability to stand against slavery without worrying about financial repercussions, helped spur the sectionalism that led to the war due to their radical anti abolitionist stance. This stance was demonstrated in 1837 by the formation of the Illinois State Anti Slavery Society, which had a largely Congregationalist base. The Society was also partly a response to the death of the Congregationalist Reverend Lovejoy who was killed trying to defend a press speaking against slavery in Illinois in 1837. The denomination’s followers were also concentrated in areas where Republicanism first developed, resulting in a strong Puritan and Congregational strain within the Republican demographic that pushed President Lincoln into office. During the war, several Congregationalist ministers in Illinois were also heavily involved with the Underground Railroad and many were even prosecuted for their efforts. The war aims of Congregationalists in Illinois were set forth during the 1864 convention of the Congregational Conference of Illinois and included the legal abolition of slavery, diplomatic relations with Haiti and Liberia, admission of African American men into the army, and the defeat of a new Illinois constitution which would perpetuate the legal discrimination of people of color. Directly after the Civil War, population and economic growth in the Northern states led to the creation of several new Congregational churches in Illinois.

The foundation of the Chicago Congregational Association in 1853 was also heavily influenced by the strict abolitionist stance held by members of the denomination. Unwillingness to abide by a Presbyterian church’s policies regarding slavery led to Congregationalist members breaking off and forming the first Congregational Church in Chicago. This same situation played out throughout the city, leading to the formation of the city’s Congregational association. The Congregationalist abolitionist movement also became centralized in the Chicago Congregational Association due to the Chicago publication of “The Western Citizen,” a well known anti slavery periodical. In 1855 the Chicago Theological Seminary was established in an effort to produce more home grown ministers for Illinois and the Western Frontier. Besides participating in the abolitionist movement, members of the Seminary responded to the influx of European immigrants to Illinois by teaching theological and bible courses in several languages. By 1890, CTS was the second largest seminary in America and the majority of ministers in Illinois that received a seminary education came from CTS. Also by 1890 and due in part to the development of the urban areas around Chicago, the Chicago Congregational Association contained more than one third of Congregational membership in Illinois and more than one third of church property values for the entire state. The Northwestern Association was established in 1861. In 1868, the Association merged with the Geneseo Association to form the new Rock River Association. The Aurora Association was formed in 1867, and the Springfield Association was established in 1886. Soon after in 1892, the Illinois German Congregational Conference was formed, although this group also belonged to the German Conference. In 1872 the state Conference also created the Home Missionary Society of Illinois, an auxiliary branch to the National Missionary Society. Soon after, in 1880, the Congregational Conference finally achieved its goal of financial independence from the American Home Missionary Society and the Eastern Congregational Associations. The Conference also pushed toward the creation of more seminaries in the state, leading to the creation of one seminary in the Southern Association and one in the Rock River Association. In 1885 the Conference also approved the creation of the Illinois Women’s Missionary Society.

In 1926, the Bureau and Rock River Associations merged to create the Bureau-Rock River Association. The Rockford and Elgin Associations also merged in 1926, establishing the Northern Association. The Northern Association also absorbed the Northern Christian Conference in the same year this new Conference was formed, in 1931. The Southern Illinois Christian Conference formed in 1931 but withdrew in 1937. The Illinois Christian Conference also formed in 1931, but was renamed the Fairfield Congregational Christian Association in 1933. In 1964, the Illinois Conference of the United Church of Christ was formed through the consolidation of the North Illinois Synod of the Evangelical and Reformed Church and the Congregational Christian Conference of Illinois. This merger led to the dissolution and reorganization of several Illinois Congregational Associations.