Witnesses say some fans screamed, ducked, or dropped to the ground after the sounds were heard at the end of "Kill You", Billboard reports.
But others on social media defended Eminem, saying that the rapper had been incorporating the noise in his performance for years and that the song is called "Kill You" - so concert goers should know what kind of content to expect from him.
"[Eminem] has used this effect - as have hundreds other artists - in his live show for over 10 years, including previous USA festival dates in 2018 without complaint", the rep said.
In one video taken during the set, a fan immediately dropped their phone upon hearing the sound effect, which was accompanied by a bright flash from the stage.
You can hear the sound effect right here.
Terror Panic ensued during the 8 Mile star's performance of his song Kill You
"Being at a festival/concert in these current times brings new concerns & fears", Williams tweeted.
Eminem, 45, chose the wrong sound effects for his headlining performance at Bonnaroo on June 9. "Would have been good to have a warning before show".
Many fans were also quick to point out the gunshot sound effects have been a regular aspect of Eminem's live shows and music for years.
Eminem is yet to comment, however, many Slim Shady fans stood up for the legendary rapper as they rebutted the sounds have always been a part of his set, while he's long lobbied for gun control in the US.
The sound effects were particularly tone-deaf considering that concert-goers are already on edge following the horrific mass shooting at the Route 91 country music festival in Las Vegas last October. This is the reality we are living.
Eminem uses loud gunshots in the show and people are not chill about it. Want him to go.
Taylor Swift lauds Manchester's 'incredible resilience' during United Kingdom gig
Charli XCX opened Taylor's Reputation show on Saturday night in a sheer PVC two-piece ensemble, and performed a range of her hits. For all the drama though, the tough-girl persona Taylor puts on through this latest album softens as she steps out in person.