The singer, 52, was denied bail on the grounds that he was a flight risk. He will be kept in custody pending trial.
The musician is already awaiting trial for more than 20 other alleged sexual crimes – all of which he denies.
For two decades R. Kelly, real name Robert Kelly, has been accused of different sexual abuse allegations.
He has consistently denied the claims.
The musician was arrested last month, and two separate federal indictments were later filed against him in Chicago and Brooklyn.
Prosecutors allege that the star and his associates recruited and transported underage girls over state lines for illegal sexual purposes, including the production of child pornography.
They also accuse him of conspiracy to obstruct justice by destroying evidence and bribing or threatening witnesses.
The current cases against him were triggered by the six-part documentary, Surviving R. Kelly, which was broadcast in the US at the start of 2019.
R. Kelly has stood trial on sexual offences once, being acquitted of child pornography charges by a jury in 2008.