Blanchard lectured in the region for the next two years. In 1860, Blanchard was named president of the Illinois Institute, a small college in Wheaton, Illinois founded a few years earlier by Wesleyans. When Warren L. Wheaton donated his farmland to the college later that year, Blanchard renamed the school after him and it became known as Wheaton College. Under Blanchard's leadership, the school was remodeled after Oberlin College, a school that was open to all students and that taught both a classic curriculum and radical social ideals. Blanchard would allow African-American students at Wheaton College to board in his house. His anti-Masonry views prohibited the founding of fraternities or sororities on campus. Blanchard believed that morality and Christian beliefs were innately experienced by man; this put him in line with most Scottish Common Sense Realists. Blanchard saw Wheaton College "as an 'arsenal' and 'drill camp' for the hosts of righteousness in the moral warfare of the world . . . a means of training social activists . . . ." In 1861, Jonathan Blanchard organized College Church in Wheaton. The church first met on the campus of Wheaton College as "The First Church of Christ in Wheaton." Blanchard wanted the church to be known for its opposition to slavery, secret societies, and alcohol use.