"The girls were 15, 16. When they went to the bathroom, Tina (Knowles, Beyonce's mother) would go with them. They did not leave our eyes," Knowles said.
Destiny's Child did eventually record a song written by Kelly, 1999's Stimulate Me, but a source told Metro the rapper was not in the room with the girls when the song was recorded.
The song also only appeared on the soundtrack for Eddie Murphy's film Life as "Mathew didn't want it on any official Destiny's Child albums".
This week US police launched a new investigation into Kelly after scores of allegations were made against the rapper in a new TV documentary series.
In Surviving R Kelly , numerous women allege they were sexually abused, coerced into threesomes, held prisoner, impregnated and beaten for looking at other men — claims which Kelly has denied.
Many of the singer's former collaborators have come forward to denounce the rapper, including Lady Gaga, who worked with Kelly on 2013 single Do What U Want.
Gaga released a statement on Twitter revealing she would be pulling the song from circulation and she stands "behind these women 1000 per cent".