Joshua Vallow and Tylee Ryan were 7 and 17 respectively when they disappeared.
Daybell was also indicted on a charge of first-degree murder in the death of his former wife Tammy Daybell.
"Local, state and federal law enforcement professionals and local and state prosecutors have worked tirelessly for nearly a year and a half to gather the facts and evidence necessary to bring forward charges on behalf of Tylee, JJ and Tammy," Fremont County Prosecutor Lindsey Blake said in a statement.
"Due to the ongoing safety restrictions imposed by the courts during the pandemic, we just recently were given permission to present information to the Grand Jury for their review. They deliberated and determined there is probable cause to believe that the Daybells willfully and knowingly conspired to commit several crimes that led to the death of three innocent people."
Attorneys for Vallow and Daybell did not immediately return a request for comment.
Tylee was last seen on Sept. 8, 2019. Police were able to find a photo from that day of Tylee on a trip with Vallow, Vallow's brother, Alex Cox, and Joshua to Yellowstone National Park, according to authorities.
Joshua, who had special needs, was last seen alive on Sept. 23, 2019 at Kennedy Elementary School in Rexburg. When police went to Vallow's home to conduct a welfare check at the prompting of his grandmother in November, Joshua was nowhere to be found.
But Vallow and Daybell had never reported the children missing and did not cooperate with investigators before they fled the state, Rexburg police said.
They were found in Hawaii in January 2020, at which point authorities gave Vallow until the end of the month to "physically produce her children." She did not, and was charged with two counts of desertion and nonsupport of dependent children.
Daybell had previously been charged with two felony counts of conspiracy to commit destruction, alteration or concealment of evidence and two felony counts of destruction, alteration or concealment of evidence. He pleaded not guilty to these charges.
Vallow had previously been charged with misdemeanor resisting or obstructing officers, criminal solicitation to commit a crime and contempt of court. She pleaded not guilty to those charges.
Daybell, a self-published author who has written more than two dozen books about near-death and doomsday events, and Vallow married weeks after Daybell's first wife, Tammy Daybell was found dead in her home in October. She was 49.
Tammy Daybell's death was initially ruled as natural but has since been classified as suspicious, and her remains were exhumed so an autopsy could be conducted. An autopsy was completed in February of this year, but authorities in Utah and Idaho did not release it due to an ongoing investigation.
Vallow's fourth husband, Charles Vallow, also died in 2019. He was shot to death by Vallow's brother, Alex Cox, in July during a confrontation in Chandler, Arizona. Cox claimed self-defense. The Maricopa County Medical Examiner in Arizona ruled the death a homicide.
Vallow and Cox were questioned by police but not charged. Cox died in December, The Associated Press reported.
Before Charles Vallow died, he filed for divorce, claiming in documents that his wife believed she was reincarnated and was a god sent to lead people during the second coming of Christ in July 2020, and she told her husband that if he got in her way, she would kill him.
Vallow's third husband and Tylee's father, Joseph Ryan, also expressed "real and serious concerns" in court documents in the midst of their divorce and custody battle. The documents said Vallow was ordered to undergo a psychological evaluation after she told social workers that “death would be an option before giving Tylee to her father, Mr. Joseph Ryan, even for a visit.”
Ryan died of an apparent heart attack in 2018. An online obituary said Ryan was 59.
This story first appeared on NBCNews.com.