Attorney Chris Bergstrom's office, which represents Geddert, and the Michigan attorney general's office confirmed his death to ABC News.
"My office has been notified that the body of John Geddert was found late this afternoon after taking his own life," Michigan Attorney General Dana Nessel said in a statement Thursday afternoon. "This is a tragic end to a tragic story for everyone involved."
Michigan State Police stated Geddert's body was located by troopers at the rest area near the I-96 highway in Clinton County at 3:24 p.m. Police would not comment on the cause of death and said the investigation is ongoing.
The 63-year-old coach was charged with 24 felonies Thursday in Eaton County, Michigan. He was accused of physically, emotionally and sexually abusing gymnasts he coached at his gym, Twistars gymnastics club in Dimondale, Michigan, according to the complaint.
Geddert had been expected to turn himself in at 2:15 p.m. to the Eaton County Sheriff's Department.
His young athletes were allegedly subjected to "excessive physical conditioning, repeatedly being forced to perform even while injured, extreme emotional abuse and physical abuse, including sexual assault," Nessel said at a Thursday press conference announcing the charges.
As a result, the victims suffered eating disorders, suicide attempts and self-harm, Nessel alleged.
According to the complaint, Geddert was also accused of sexually assaulting a teen with his hands in 2012 and lying to investigators when he claimed that he never heard anyone complain about his associate Larry Nassar, the Olympic team doctor who was convicted of sexually abusing young female athletes.
In 2018, Nassar was sentenced to up to 175 years behind bars for his decades of abuse after more than 150 survivors and family members testified against him.
Geddert and Nassar worked closely for decades and both rose to prominence in the gymnastics world. Nassar worked with gymnasts at Twistars, where hundreds claimed he sexually abused them.
Geddert faced 20 counts of human trafficking and forced labor causing injury, one count of racketeering, two counts of criminal sexual conduct for assaulting a girl under the age of 16 and one count of lying to a peace officer.
His lawyer did not respond to ABC News' request for comment on the charges.
Geddert had been under investigation for three years, after victim impact statements shared at Nassar's sentencing hearings claimed Geddert knew about the abuse.
Rachael Denhollander, the first woman to publicly accuse Nassar of sexual assault, spoke out about Geddert's death Thursday, saying there was "so much pain and grief for everyone."
"To the survivors, you have been heard and believed, and we stand with you," Denhollander wrote on Twitter. "Thank you for telling the truth. What you have done matters. Please stay safe, you are loved and wanted here."
Aly Raisman, a two-time Olympian who won six Olympic medals in total and was a member of the "Fierce Five" in 2012 and "Final Five" in 2016, spoke out regarding Geddert's death Thursday night.
"As a minor on the National Team, I frequently had to travel (without my parents) under the supervision of USA Gymnastics. The 'responsible' adults included John Geddert, Marvin Sharpe, Steve Penny, and Larry Nassar," she wrote on Twitter.
"Respectively, the criminal offenses they have been charged with include Criminal Sexual Conduct and Racketeering, Child Molesting, Destroying Evidence, and Sexual assault. For an organization that has claimed for the past 15+ years that 'athlete safety is the No. 1 priority,' it's impossible to imagine a greater failure," she added.
Raisman was coached by Geddert for the 2012 Olympics and was one of the high-profile gymnasts who accused Nassar of sexual abuse.
"This is & has always been bigger than John Geddert, Marvin Sharpe, Steve Penny, and Larry Nassar," she continued on Twitter. "Why is there still no independent investigation? How many more children have to suffer?"
She is the only member of the "Fierce Five" who has publicly addressed Geddert's death as of Thursday night.
Jordyn Wieber, another member who was coached by Geddert, is celebrating "women's empowerment" this week with the Arkansas Razorback Gymnastics team, for whom she is the head coach, according to the team's Instagram.
"Sick to my stomach. Thinking of the survivors out there. Wish there was more I could say to ease the pain & suffering," Raisman wrote in her final tweet of the night.
ABC News' Rachel Katz and Celia Darrough contributed to this report.