In 1990, the four million dollar renovation work on the museum was completed. This renovation included adding airconditioning and humidity control to the building, as well as new gentle lighting that would be kinder to the collections, and sound-cushioning carpet to reduce the noise of footsteps in the exhibits. School children had mounted a campaign to save Morrill Hall in 1986 and 1987, by writing to their state senators and lobbying for a bill to finance the renovations. In thanks, the museum held a picnic celebration for the schoolchildren and their families.

As the 1990s continued, the museum began a new focus on helping Nebraskans recognize the history of the land around them. Education on fossil hunting and identification was renewed, resulting in more private citizens stumbling upon finds, and donating them to Morrill Hall's collections. Given the rich fossil record of the state, many visitors not only learned from the "fossil hunting" displays, but were able to recognize the deep ecological history Nebraska has had.

In 1993, Morrill Hall had to close the gift shop in the museum, as there was no money to hire a permanent employeed. Debate between the university and the museum grew as to whether the museum should be run by volunteers, as the Sheldon museum gift shop was, or be run by the Friends of the Museum organization. Another point of contention was where the profits from the gift shop ought to go: to the museum directly, or to the university? This debate raged on for over half a year, before it was decided that the Friends of the Museum would take over the gift shop and its funds.

Research into Morrill Hall's past also began coming to light, as the museum's publication, "Museum Notes" featured articles on various previous directors of the museum, as well as early Nebraska paleontologists and geologists. Today the museum continues to be a popular institution for school field trips and group outings, as well as frequented by Lincoln residents and students of the university. Their research has even made it to the national stage, as UNL's Morrill Hall contributed to the latest exhibit, "Titanoboa", in the Smithsonian museum of natural history.