In June of 1884, the University of Nebraska offered Charles Bessey the professorship of botany, but Bessey respectfully declined due to his extensive research in Ames, as he did not want to rebuild from the ground up again and felt Nebraska was not ready for him. However, another offer was made two months later in August of 1884, but this time Bessey was offered not only the professorship, but also the deanship of botany (Volta). After another visit to the University of Nebraska and further consideration, Charles Bessey accepted this offer. He gave the inaugural address just one month later in September of 1884 and began his work as a professor, researcher, and dean in January of 1885.

Charles Bessey was known for his wonderful teaching methods and being a favorite professor for most of his students.  Bessey’s major contribution while at UNL was to his students. In his 45 years of teaching he taught 4,000 of them, and 800 are said to have achieved national reputations in the botany field (Bejot). He was described to be extremely engaging and had an unrivaled love for the subjects he taught. 

Today, there are a few Professorships in Bessey's name. The University of Nebraska–Lincoln has established the Charles Bessey Professorships to recognize distinguished scholarship and creative activity (Walsh). The first Bessey Professors were named during the academic year 2001-2002. Here is a list of the recipients of this honored Professorship: 2002- Shashi Verma, Svata Louda, Clinton Jones, and Peter Dowben; 2003- Robert Spreitzer, Stephen Ragsdale, Martin Dickman, and David Cahan; 2004- James Specht and James Takacs; 2005- Vladim Gladyshev and Majorie Langell; 2006- Allan Peterson, Anthony Zera, and David Hage; 2007- Hendrik Viljoen; 2008- Blair D. Siegfried; 2009- Patrick Dussault and Evgeny Tsymbal. Only a limited number of these Professorships are given out each year, and "Bessey Professors" receive a $5,000 annual stipend.

Along with the Bessey Professorship, UNL also commemorates Charles Bessey today with the Bessey Medal. The Bessey Medal is presented by UNL in recognition of distinguished achievement in the sciences or fields grounded in the sciences. This medal is named after Charles Edwin Bessey, who was one of the world's pioneers in botany. Bessey is often credited with originating ecology as a field of scientific inquiry. The first Bessey Medal was awarded to Alan J. Heeger on October 10, 2001. The latest Bessey Medal was awarded to astronaut Clayton Anderson in 2010.

As Charles Bessey continued his work as a professor, researcher, and dean at the University of Nebraska-Lincoln, he began to become more important to the University and worked his way up on the University's "totem poll". Bessey added to his previous positions by being appointed chancellor of UNL three different times.

The first of these times was in 1888 after Irving Manatt, the previous chancellor, was dismissed from his position. At first, Bessey refused to accept the chancellorship permanently because his overwhelming interest was found  in plant research and teaching (Knoll, 21). Bessey was chancellor until June of 1891 when James Canfield replaced him. Eight years later, in August of 1899, George MacLean resigned from chancellor and Bessey was once again appointed chancellor. One year later, E. Benjamin Andrews took over the position of chancellor for the University. However, for 3 months of  that summer Charles Bessey was once again named chancellor while Chancellor Andrews took a leave of absence. After those three months, Chancellor Andrews took over once again and this would be the last time Charles Bessey would have the title of chancellor. In all of his stints as chancellor, Bessey knew that he would never be at the position for a long period of time. However, he did his part to help the University when it was "in between" chancellors (Wolfe, 2).