Caliph Basha ibn-Abdur Raheem, 29, had all charges against him dismissed by District Judge Leonie Brinkema, who also threw out several conspiracy and firearms charges against two other defendants Seifullah Chapman and Hammad Abdur-Raheem.
Masoud Khan, the other defendant facing the most serious accusations, also had a lesser charge dismissed.
He however is still charged with conspiracy to wage war against the United States and conspiracy to provide support to Usama bin Ladin's al-Qaida.
Caliph Abdur-Raheem's mother wept when Brinkema announced her ruling.
"I knew I didn't do anything," Abdur-Raheem said. "I always try to do everything by law."
Prosecutors had alleged that Abdur-Raheem's possession of an AK-47 style rifle and his participation in paintball games with group members in 2000 and 2001 were sufficient participation in the alleged conspiracy to allow the case to move forward.
But the judge disagreed, finding little evidence in the two-week trial.
"He does subscribe to perhaps a more radical form of Islam. He did go and participate in paintball…but playing paintball itself is not an illegal activity," Brinkema said.
Abdur-Raheem said the charges against all the defendants were baseless.
The government alleges some of the conspirators, including Khan, joined a "militant Islamic group" in Pakistan shortly after the 11 September 2001 attacks with the ultimate goal of fighting for the Taliban against the US attack on Afghanistan later the same year.