The 21-year-old former soldier is due to appear in Westminster Magistrates’ Court on Monday. He was arrested on a towpath in Northolt after being pulled off a bicycle by a plain-clothed officer.
Mr Khalife escaped from the prison on Wednesday morning, seemingly by hiding under a food delivery lorry.
The Met Police said he had been charged with escaping on September 6 while on remand at HMP Wandsworth Prison awaiting trial at the Old Bailey, contrary to common law.
He was being held on remand at the prison in south-west London after previously being charged under the Official Secrets Act and the Terrorism Act.
Mr Khalife is accused of trying to spy for an enemy state, understood to be Iran, and obtaining information likely to be useful to a person committing or preparing an act of terrorism. He is also charged with plotting a fake bomb hoax at MOD Stafford, where he had been based. He denies the charges against him.
His escape prompted questions about security at Wandsworth prison, with Justice Secretary Alex Chalk telling the BBC he has launched investigations into the incident.
Mr Chalk says preliminary inquiries into the getaway have determined that correct security protocols and staffing levels were in place at the time.
Speaking to the BBC’s Sunday with Laura Kuenssberg, he said: “The real question is whether the protocols were followed to the extent they should be.”
The minister also revealed earlier that dozens of prisoners were moved from HMP Wandsworth to other prisons after the escape, “out of an abundance of caution”.
Mr Chalk told the BBC that “approximately” 40 inmates on remand were transferred this week, amid questions about whether Mr Khalife should have been held on remand at the Category B jail.
Police had offered a reward of up to £20,000 for information leading to Mr Khalife’s arrest and detectives said they had received more than 100 calls from people offering information.
He was detained at 10:41 BST on Saturday – about 14 miles from the prison.
