During the 1850s, Reverend Alonzo Church, a Presbyterian minister and a graduate of Middlebury College in Vermont, was the president of the university. Church began his career at the university as a mathmetician and in 1829 became its president. He remained in the post for thirty years, the longest term in the university's history. Because of his focus on student discipline, Church clashed with the student body, and periodically throughout his presidency, campus unrest erupted.

During the Church years, incoming students were expected to have a background in latin and greek literature, grammar, geography, and mathematics as well as a knowledge of the Bible. According to the 1852-1853 Franklin College catalogue's outline of admission requirements,

a candidate must have a correct knowledge of Cæsar-- Cicero's Orations-- Virgil, John and the Acts in the Greek Testament-- Græca Minora, or Greek Reader-- Latin and Greek Prosody-- English Grammar-- Geography-- Arithmetic, and Algebra through Simple Equations.

Surveying; Navigation; Levelling; Natural Philosophy; Evidences of Christianity; Greek . . . Analytical Geometry; Conic Sections; Natural Philosopy; Rhetoric . . . Cicero de Oratore; Differential and Integral Calculus; Natural Philosophy; Moral Philosophy; Chemistry; Logic.

While at the university, students were expected to abide by established rules and regulations. The faculty was responsible for student discipline. Students were required to attend Chapel every morning and evening during the week and their own church on Sundays. Gambling, disorderly conduct, cursing, fighting, dueling, drunkenness, card games, billards and circuses were all forbidden. Students were not permitted to have dogs, servants, guns, pistols, daggars, or swords. The most common offenses were drunkenness and disorderly conduct. In 1852, student fees ranged from $168.50-$204, the bulk of which paid for nine and a half months of room and board. Also included in the fees were tuition, servants, a library fee, washing, and fuel. In today's dollars, tuition was the equivalent of $3850-4650.

During the 1850s, enrollment and faculty numbers began to drop off. A $6000 decrease in state allocations during the 1840s led to the decline. During this period, there was a large turnover in staff. Many of the older faculty members had left and newer younger ones were hired to replace them. These new faculty members came into conflict with President Church over his disciplinary policies. Church felt the faculty was too lax with the students. As a result of the conflict, several bright and well respected professors resigned including Professor Charles F. McCay and the LeConte brothers.

Faced with staffing problems and dwindling numbers, the Board of Trustees formed a commission to address the problems. In November 1855, the commission furnished its recommendations for reorganization in the form of the Mitchell Report. They proposed dividing the College into four major divisions: science, teacher education, law, and agriculture. The student body would be split into two seperate colleges-- freshmen and sophomores would become part of the new Collegiate Institute and the remainder would attend the older Franklin College. The commission also recommended the addition of a modern languages professor to the faculty. With the retirement of President Church in late 1859, the trustees decided reorganize the university further. The university would be headed by the chancellor, and both the Collegiate Institute and Franklin College would be led by their own vice chancellor or president. This decade of reorganization was the stepping stone for entry into the world of modern universities.