Cook County State's Attorney Kim Foxx has said her office "will no longer be pursuing these indictments" and will ask a judge to dismiss those charges.
"Sometimes justice is served even when there is no conviction," she said.
The charges date back to as far as 1998.
Kelly, 56, was convicted in 2021 on racketeering and sex trafficking charges, and sentenced to 30 years in prison.
Last year, he was also convicted on sex crimes charges for which he is scheduled to be sentenced next month and likely won't be allowed for release until he is 80.
Cook County State's Attorney Foxx announced the state's case in 2019, saying the incidents occurred from May 1998 to January 2010. Illinois has no statute of limitations on child sex abuse charges.
But federal prosecutors in Chicago and New York moved more briskly to file indictments and along with Covid-19 delays, the Cook County courts were slowed.
"Due to the extensive sentences that these convictions hold, our office has decided not to continue to expend our limited resources and court time with the indictments that we previously charged Mr. Kelly," Ms Foxx said.
She said resources will be put to better use to prosecute other sexual offenders.
In 2019, Ms Foxx had urged victims to come forward in order to bring charges against Kelly.
Lanita Carter, who came forward in 2019, objected to this decision to drop charges.
"I have spent nearly twenty years hoping that my abuser would be brought to justice for what he did to me," she said, "With today's announcement, all hope of justice for my case is gone."
Kelly also faces a sexual misconduct case in Hennepin County Minnesota, but that case has been paused during the ongoing federal cases as well.