Umar Ahmed Haque, 24, and Muhammad Abid, 27, both from Newham in east London, were arrested on 17 May along with Abuthaher Mamun, 18, from Barking.
They have been remanded in custody and will appear before Westminster magistrates on Friday.
A fourth man, Nadeem Ilyas Patel, 25, from Newham, faces a charge of conspiring to possess a firearm.
Mr Haque has been charged with preparing to commit acts of terrorism and four counts of possessing records useful for committing or preparing acts of terrorism.
Mr Abid has been charged under terror laws with failing to disclose information and Mr Mamun is accused of assisting another to commit acts of terrorism.
Three men from London have been charged with offences under the Terrorism Act over an alleged UK terror plot.