Peter Moses Jr., 28, was indicted last year on first-degree murder charges in the case. His guilty pleas mean he will avoid the death penalty.
Prosecutors say Moses killed 4-year-old Jadon Higganbothan and 28-year-old Antoinetta McKoy.
Their bodies were found buried in plastic bags by a plumber working in the backyard of a home in the 2600 block of Ashe Street last summer.
McKoy and Higganbothan lived with a polygamist religious group led by Moses known as the "Black Hebrew Israelites."
At a court hearing last year, Durham District Attorney Tracey Cline said Moses believed the boy was homosexual and that was unacceptable to his religious beliefs. She said Moses shot Higganbothan in the garage of a home on Pear Tree Lane in front of his mother.
Cline said investigators believe McKoy was killed because she tried to escape from the group and it feared she would tell police about the murder.
According to search warrants obtained by ABC11 earlier this year, investigators found two of Moses' fingerprints on tape used to secure the plastic around the bodies.
Six others are charged in the case along with Moses Jr., including Higganbothan's mother 25-year-old Vania Sisk, 40-year-old Lavada Quinzetta Harris, and 40-year-old Larhonda Renee Smith. They did not enter pleas Monday.