Additional Sessions Judge Sidharth Sharma framed charges of criminal conspiracy under the Indian Penal Code and other offences under the Unlawful Activities (Prevention) Act against Bhatkal, his aide Asadullah Akhtar and other IM operatives.
After the accused pleaded not guilty and claimed trial, the court listed the matter for October 23 for recording the statements of prosecution witnesses.
The court observed that Akhtar and Yasin Bhatkal were those who conducted a recce of Jama Masjid area.
The prosecution had said Akhtar was present at the spot while Bhatkal was in touch with other accused on phone as call detail records showed regular conversation between him and other co-accused persons.
Bhatkal will also face trial under the Explosive Substances Act in one of the cases.
The court also framed charges of criminal conspiracy, attempt to murder, voluntarily causing hurt, common intention of the Indian Penal Code and terror act, conspiracy and being a member of banned terror organisation under the Unlawful Activities (Prevention) Act and under the Arms Acts against Mohammad Adil, accused of firing upon foreign nationals at Jama Masjid in 2010.
The court has issued production warrant against Ajaz Shaikh, who is accused of sending email claiming that the attack was carried out by Indian Mujahedeen on September 4, 2010.
Shaikh is lodged in Taloja Jail in Mumbai and was not presented before the court on Tuesday.
Beside, other accused in the case are Zia-ur Rehman alias Waqas, Gauhar Aziz Khomani, Gayur Ahmad Jamali, Mohammad Irshad Khan, Mohammad Aftab Alam and Kamal alias Bilal.
The court on August 1 discharged accused Syed Ismail Afaaque, Abdus Saboor, and Riyaz Ahmad Sayeedi in the 2010 Jama Masjid blast case on the ground that it did not find any evidence against them.
Proceedings against one accused was dropped after his death.
On September 19, 2010, two motorcycle-borne persons fired at tourists outside Jama Masjid in Old Delhi, injuring two Taiwanese. A mild explosion in an abandoned car also occurred in the area.
Two cases were registered against IM members, including module co-founder Yasin Bhatkal, its chief Riyaz Bhatkal and Iqbal Bhatkal, for attempt to murder, voluntarily causing hurt and criminal conspiracy and under the Unlawful Activities (Prevention) Act and the Arms Act.
Riyaz Bhatkal and Iqbal Bhatkal are on the run.
Yasin Bhatkal, arrested along with Akhtar from the India-Nepal border in August 2013, topped the Delhi Police list of 15 most-wanted terrorists involved in bombings across the country.