In 1834, the academy was chosen by the New York State Legislature to exclusively offer a teacher education program for its senatorial district.

With funds from the state, and from support by preceptor Reverend Asa Brainerd, the first diploma in teaching was given in 1836, thus beginning the academy's and eventually the college's longstanding tradition of excellence in the field of teacher education.

In 1964, the college's mission changed to providing multiple programs, and the university adopted its current name.

Known as the Potsdam Miracle, Stephens transformed a practically non-existent department to having the third largest number of mathematics majors of any institution in the United States during his tenure.

In response to declining enrollment, in September 2023, SUNY Potsdam president Suzanne Smith announced a plan to reduce the deficit of $9 million by eliminating up to 14 degree programs over the next three to five years.

In 1981 and 1986, under Hall of Fame coach Jerry Welsh, the Potsdam Bears basketball team won the NCAA Division III national championship.

The 1995-96 men's ice hockey team won the program's only SUNYAC title in school history, under Hall of Fame coach Ed Seney.

In 2011, SUNY Potsdam athletics was placed on NCAA probation due to an inadvertent error in the awarding of international student-athlete grants.