The 57-year-old is accused of directing a terrorist organisation, being a member of a proscribed organisation and addressing meetings to encourage support for a proscribed organisation.
He was set to enter a plea at the Old Bailey yesterday but it was put back.
Appearing in grey prison uniform over video link, the preacher spoke only to confirm his identity during the hearing which lasted around one hour.
An earlier hearing was told Choudary had provided lectures to the Islamic Thinkers Society, which prosecutors said is Al-Muhajiroun “for all intents and purposes”.
Al-Muhajiroun has been banned in the UK since 2010 but it is alleged the group has continued to exist under various names.
Mr Justice Jeremy Baker remanded the preacher, from Ilford in east London, into custody and he is next due in court on a date to be fixed in March.
A provisional trial, which is expected to last up to eight weeks, has been fixed for May 20 at Kingston Crown Court.
Choudary was arrested in east London on July 17 while a second suspect, Khaled Hussein, was detained at Heathrow having arrived on a flight the same day.
Hussein, who lives in Canada, is charged with membership of Al-Muhajiroun but did not appear at the hearing on Friday.
His lawyer was content for proceedings to continue in his absence.
Proscription is the banning of an organisation based on an assessment that it commits or participates in, prepares for, promotes or encourages, or is otherwise concerned in terrorism, according to the Home Office.
