A new and exciting addition to the museum began in 1980. The Ecounter Center, a new area dedicated to young visitors of the museum, opened on June 23, 1980. This area involved much more "hands on" opportunities for visitors, by allowing them to experience the content of the museum in a novel way. "Touch boxes" allow for visitors to feel/touch specimens for themselves. The fossil box, a box fillled with sand with hidden invertebrate fossils inside, was a popular attraction. As director B. Shultz put it, "Touching and feeling, whether the specimen is alive or preserved, or inanimate, gives people a much better appreciation for its true nature." Flip cards allowed guests to find answers to common questions about specimens, while a few tanks of live insects were sometimes available for holding under the supervision of museum staff.

The encounter center led to a skyrocket in field trips from local schools, as well as schools across the state. The Nebraska School for the Visually Handicapped began bringing tour groups several times a year, as the encounter center allowed the blind children to enjoy exhibits in ways that would have been impossible previously. Even senior groups enjoyed visiting the new center. However, funding for the center was threatened several times. In the end, several organizations pitched in to secure funding to maintain the center. In 1988 annual attendance to the center topped 61,000 visitors. During much of the 1980s, the focus of the museum was on enhancing the encounter center.

In 1988, the museum failed to recieve their usual ten year accreditation from the American Association of Museums. This struck a heavy blow for Morrill Hall. Lack of long term accrediation meant that without change, the museum would be struck from the association and lose standing in the academic sphere. The association found fault with the museum's low funding, lack of exhibit programs, and lack of parking and issues with climate control and parking for the museum.

However, Schultz also prepared a large document focused on renovations and repairs to be done to Morrill Hall. Having only had patchwork repairs done since its original construction in 1927, the building need much to be done on its ventilation and ductwork. Many of the preservation and exhibit areas did not have adequate heating and cooling, or humidity control to help mainting the displayed specimens. Schultz's proposal involved the majority of the museum, with additional requests for an increase in employees to help in preservation, as well as security. Later in the decade, the museum began the four million dollar renovation, finally adding climate control to the building, vastly improving the condition and aging of the collections.