While at Clemson University, Monahan broke several school and Atlantic Coast Conference records, some of which he still holds, including game appearances, at bats, and hits. Monahan appeared in every Clemson game during his 3 years at the school. In the 1994 season, Monahan led the NCAA in hits and runs. His 137-hit season remains an ACC record. Also in 1994, Monahan set ACC single-season records of 330 at bats and 75 game appearances. He is one of only 5 Clemson Tigers to hit for the cycle, doing so in Hawai'i against Hawai'i-Hilo on March 19, 1994. He was ACC Player of the Week twice in 1994, and the ACC Tournament MVP. He was named to the All-ACC Tournament team in 1994 and 1995. In 1993, along with teammate Scott Winchester, Monahan was a Freshman All-American; in the 1994 and 1995 seasons, Monahan was a two-time All-American in the ABCA, Baseball America, Collegiate Baseball, and NCBWA polls. In 1993, he played collegiate summer baseball in the Cape Cod Baseball League for the Yarmouth-Dennis Red Sox. Monahan was a 3-time Letterman at Clemson, and was inducted into the Clemson Athletic Hall of Fame in 2011.
On December 28, 2007, Monahan admitted in an interview with ESPN that he used the anabolic steroidsDeca-Durabolin and Winstrol as well as amphetamines during his playing career. Monahan stated that he started using steroids in 1998, partly because of what he states was widespread use in the Mariners clubhouse. During the time he played with the Mariners, he played with players who were mentioned in the Mitchell Report, including Ryan Franklin, Glenallen Hill, David Segui and Todd Williams. Three players have since come out to refute Monahan's comments regarding the Mariner clubhouse atmosphere. Raúl Ibañez stated:
It's amazing to me that a guy like Shane—a guy who was up and down at best and had a very limited cup of coffee with us—would be able to know what was going on. I was up and down like he was. I was in that same boat that he was in, and everyone makes their choice. In 10 years, I've never seen a person take a steroid.
I can tell you that I was there for 10 years and I never saw anyone take steroids. This will be my 20th year in the major leagues, and I don't even know what a steroid looks like. If I have to start relying on those things, after so many years in the game, then it's time to pack it in. That's the way I look at things.
Edgar Martínez, like former teammates Raúl Ibañez and Jamie Moyer, denied allegations of such use in the clubhouse. Martínez made this statement while visiting the Mariners in spring training: