One of the victims claims that Timothy Storey, 35, raped her on two occasions while he was working at a London church. The victim alleges he attacked her once at his home and also in a street in 2002.
The second victim told the jury Timothy Storey sent her indecent messages online.
The girl says he then invited her to a concert in Birmingham, where he gave her alcohol and took her back to his accommodation in Oxford - where he was studying to become a minister - and raped her twice.
Both girls were under the age of 18 when the Mr Storey is accused of raping them.
Timothy Storey is charged with four counts of rape, one count of indecent assault and one count of sexually grooming a teenager online. He denies all of the charges.
Hanna Llewellyn-Waters, prosecuting, said the defendant engaged in "entrenched manipulation of young females to engage in sexual activity for his own gratification."
"The defendant targeted vulnerable victims and his conduct revealed a wholesale breach of trust in his position of relative power as the church youth leader.
"After gaining their confidence and trust, he made contact with them and groomed them to form inappropriate relationships with them before manipulating [them] into sexual activity."
The Church of England's previous safeguarding practices have also been highlighted in the victim's testimonies.
The trial at Woolwich Crown Court continues.
