The three men, charged with terrorist offences, live in different parts of Sweden and met in an Internet chatroom, where they planned to set fire to the Livets Ord church, said to be the largest place of worship in Europe.
The men planned to meet in person early in January to discuss their plans, but police intervened to stop them.
As they finally met each other in Stockholm district court, the three denied the charges that they planned to strike against Livets Ord.
The eldest man, aged 25, confessed through his lawyer Tomas Nilsson that they had spoken about carrying out an attack, but claimed that they would never have gone through with the plan.
Two of the men are in addition suspected of attempted terrorist offences, for throwing molotov cocktails at an Iraqi polling station in Kista, north-west Stockholm, in December 2005.
Prosecutor Tomas Lindstrand is backing up his case with evidence from Internet chats between the men.
“The men talked in the chatroom about their plans, and about the possibilities of finding the perfect bomb,” he said.