His lawyer cited a recent physical attack by a fellow inmate as a reason why the star should have been granted release on bail.
R. Kelly -- born Robert Kelly -- faces both state and federal charges in Illinois, New York and Minnesota, where his alleged offenses range from sexual assault to racketeering to child pornography and beyond.
The singer has denied all allegations against him.
Additionally, he's been deemed a danger and a flight risk, and the appeals court said prosecutors proved that "no condition or combination of conditions could assure against those risks" and that Kelly had no "compelling reason" for a temporary release.
Mike Leonard, an attorney for the Grammy winner, called the ruling "very disappointing and somewhat surprising" because it appeared that judges understood that Kelly could not prepare for trial while incarcerated.
In a Chicago federal court filing Friday, Leonard stated that Kelly suffered unspecified injuries from another inmate in late August.
He claimed the attack was proof that Kelly could not be protected by authorities, hence the request for bail.
"The so-called maxim of the presumption of innocence appears to be a misnomer" for Kelly, said Thomas Farinella, another one of the singer's attorneys. "We will continue to vigorously fight for Mr. Kelly’s vindication."
The Federal Bureau of Prisons did not immediately respond to Fox News' request for comment.
The Associated Press contributed to this report