The couple are members of the Followers of Christ Church, which embraces faith healing.
Several members have been convicted of crimes for failing to seek medical care for their children, including Sarah Mitchell's sister and brother-in-law.
The deaths prompted Oregon lawmakers in 2011 to remove faith healing as a legal defense in murder and manslaughter cases.
It was not immediately clear if the Mitchells had attorneys. Relatives hung up the phone when contacted Monday.
Chris Owen, Clackamas County chief deputy district attorney, said the pair would be arraigned Tuesday.
He declined further comment, saying the case remains under seal.
Oregon's chief medical examiner, Karen Gunson, said in March that Ginnifer was several weeks premature and her lungs were too underdeveloped to allow her to breathe unassisted for long.
Gunson told investigators that Gennifer's death would not have occurred suddenly, and that there would have been signs that the infant was having difficulty breathing including skin discoloration.
Gunson believed "the death was preventable if Baby Ginnifer had been given the medical care available in a hospital neonatal intensive care unit," the affidavit said.
Authorities said the birth was attended by about 60 people, including three midwives, family members and other church members. No one called 911 when Ginnifer struggled to breathe.
Eric Tonsfeldt, a deputy medical examiner, responded to a call about the death and noticed the surviving twin, Evelyn, was also struggling to breathe.
Law enforcement persuaded the parents to get her medical treatment.
Evelyn was taken to Doernbecher Children's Hospital in Portland and survived. It's unclear who has custody of her.
The church, which operates in Oregon and Idaho, has about 1,000 members and is rooted in Pentecostalism, although it is not affiliated with any denomination.
Members believe in a literal translation of the Scripture, which states that faith will heal all and if someone dies, it is God's will.
The church drew criticism in 1998 after The Oregonian newspaper analysed the deaths of 78 children buried in the church's graveyard since 1955.
At least 21 could have been saved by medical intervention, the newspaper found.