Bruce Leonard snr, 65, and Deborah Leonard, 59, are accused of causing Lucas' Leonard's death at Word of Life Church in Chadwicks, New York.
They both deny the charges.
The couple drove Lucas to a hospital where he died on Monday, claiming he was shot. Police have since said that he suffered blunt force trauma and not a gunshot wound.
Their other son Christopher, 17, is also in a serious condition in hospital.
Police discovered him on the second floor of Word of Life church on Monday after recording his brother Lucas' death as suspicious.
New Hartford Town Court heard that the defendants allegedly beat their sons for more than ten hours in order to get them to confess to their sins and ask for forgiveness.
Four other parishioners: Sarah Ferguson, 33, Linda Morey, 54, David Morey, 26, and Joseph Irwin, 26, have been arrested charged with second-degree assault.
They deny the charges against them.
Several children have been taken out of Word of Life Church and referred to social services for their protection.
Word of Life church, which does not appear to have a website, describes itself as a "Christian church" on its building.
Police say additional charges and arrests are still pending.
Proceedings continue.
