Timothy Storey is charged with two counts of rape and one count of assault by penetration against one of the girls, and two counts of rape against another girl. He is also charged with one count of sexually grooming a 13-year-old girl.
Mr Storey denies all the charges against him, and has previously told Woolwich Crown Court that the activity he had with the two girls was consensual.
The alleged offences happened while he was working as a youth leader for the Diocese of London and training to become a minister at the University of Oxford.
A spokesperson for the Diocese of London has previously said: "The Diocese of London first received complaints regarding Timothy Storey's alleged conduct in early 2009.
At the time he was training as a Church of England ordinand at Wycliffe Hall. The Diocese's Child Protection Adviser at the time looked into the allegations and spoke with the Metropolitan Police Westminster Child Protection Team, raising concerns that his actions were an offence under the 2003 Sexual Offences Act.
"Whilst the Diocese's Child Protection Adviser said police did not believe any criminal act had been committed, the Diocese nevertheless took the decision to withdraw him from ordination training. The Diocese subsequently submitted a report to the Independent Safeguarding Authority (now known as the Disclosure and Barring Service).
Within the submission, the Diocese stipulated that it deemed Timothy Storey's behaviour to pose a risk to those under the age of 18 and included witness statements that the Diocese gathered from a number of individuals who had made allegations against Mr Storey.
The National Church of England was also notified, to prevent him from applying for ordination elsewhere in the country."
Jurors are expected to deliver their verdict at 10 o'clock.
