Daniel Khalife, 21, is accused of absconding from London's Wandsworth prison on September 6, allegedly by clinging to the bottom of a delivery van.
Following a huge manhunt, he was rearrested three days later on a canal towpath in west London after being pulled off a bike by a plain-clothes officer.
Khalife appeared at London's Old Bailey court via video-link from the high security Belmarsh prison wearing a blue and yellow sweatshirt.
"I am not guilty," he told the court.
Khalife had previously been in custody awaiting trial on suspicion of gathering information that could be useful to enemies of the UK.
He was also charged with gathering information of use to "a person committing or preparing an act of terrorism".
He was additionally charged with a bomb hoax for allegedly placing a suspect device at a Royal Air Force base.
Khalife, who was discharged from the army in May, had denied the three charges at an earlier hearing.
He is due to stand trial at Woolwich Crown Court from November 13.
He will reappear at the Old Bailey on October 13.
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