[1][2] Under his administration, the student body and faculty more than doubled in size, and the school went from an academy to a university, and was officially incorporated by the Church of Jesus Christ of Latter-day Saints.

Cluff changed class periods from half an hour to a full hour, adopted the official colors of the university, started summer school and the Alumni Association, encouraged the university's first student newspaper (White and Blue), provided the first student loans, and developed an intercollegiate sports system.

He worked closely with professors in the fields of astronomy and engineering, and became good friends with James Burrill Angell, president of the university.

At the time he left for the University of Michigan, Cluff had two wives, Mary the daughter of David John and Harriet "Hattie" Cullimore.

[citation needed] After receiving his degree, Cluff returned to Brigham Young Academy and became the assistant principal.

By late 1891, Karl G. Maeser had to be replaced as principal of Brigham Young Academy because he had been called to oversee the entire LDS education program as superintendent of church schools, and was unable to do both jobs.

[3]: 239 In 1893, Cluff went back to the University of Michigan to work on a master's degree and left George H. Brimhall as acting president.

He began separation of the college from the high school, giving older students access to higher level materials.

[4]: 29  The Collegiate Department of Brigham Young Academy was officially established in 1896 and was an extension of the college-level courses that Cluff had been teaching since becoming principal.

Another recurring problem was the academy's teacher retention because of mission assignments from the church that required the instructors to leave their teaching jobs and dedicate all of their energies to their missionary efforts.

In order to accomplish this goal, Cluff started a "Normal Training School" which gave free lessons to students who were interested in teaching.

[3]: 263–264 In May 1898, College Hall was built in order to provide more space for the upper division students of the academy's Collegiate Department.

[3]: 271 In 1899, Cluff outlined his proposal to take Academy students on an expedition to ancient Book of Mormon ruins and complete other related historical studies in Central and South America.

[3]: 294  After leaving predominately Mormon areas, members of the expedition began to go off in pairs to act as missionaries in the cities that they passed through.

Once he returned to Utah to report his findings, the First Presidency and Quorum of the Twelve Apostles decided that because the members of the expedition were not well experienced travelers and were not proving to be completely compliant with the rules that they were taught at the academy, a letter was sent to Joseph F. Smith.

After nearly two years of travel, the expedition ran out of supplies, had problems with securing safe passage through Colombia, and was forced to turn back.

Cluff finally returned to his position in 1902, but was accused of various improprieties, including sexual immorality by his assistant Walter Wolfe.

[7][3]: 323  The charges of immorality stemmed from a post-Manifesto marriage between Cluff and twenty-five-year-old Florence Mary Reynolds conducted in Mexico.

[8][9] In Cluff's last official act, he proposed to the board that the academy be named "Brigham Young University".