Officers discovered the five during a raid in the desert of New Mexico last August while investigating the disappearance of a three-year-old child several months earlier.
Siraj Ibn Wahhaj, 40, his girlfriend Jany Leveille, 36, a Haitian woman allegedly in the US illegally, her two sisters and her brother-in-law, were indicted on Wednesday by a grand jury.
The indictment identified the other accused as Hujrah Wahhaj, Subhanah Wahhaj and Lucas Morton.
The charges relate to terrorism, kidnapping, and conspiracy to provide resources, training and other support for "attacks to kill officers and employees of the United States," the Department of Justice said.
According to the indictment, the five adults had, from October 2017, "maintained a training compound to prepare for attacks on government, military and other institutions."
Siraj Ibn Wahhaj and his girlfriend "instructed persons, including other occupants of the training compound, to be prepared to engage in jihad, to die as martyrs and to engage in violent acts," including the killing of FBI employees and military personnel, the document alleges.
Siraj Ibn Wahhaj was the father of the missing child, whose body officers allegedly discovered buried under rubbish. They also found 11 other minors, alive but dirty and wearing rags.
The "training compound," entrenched in the ground and built from plastic tarps and tires, contained about a dozen firearms, munitions, a firing range, and a tunnel leading outward.
But there was allegedly no water, food or electricity.
The adults are also charged with kidnapping the child, identified only as "John Doe," and hiding him "resulting in his death."
According to other court documents, the boy had a brain injury and suffered seizures.
Leveille, who believed in "black magic," allegedly wanted to "exorcise" him.
The other minors were the children of the three women.
Authorities said last year that the raid was carried out after the discovery of a web posting from one of the women inside the compound who said the group was starving.