A federal grand jury indicted Yassin Aref and Mohammed Hossain late on Thursday on nine new charges each, including conspiracy to provide material support to Pakistani-based Jaish-e-Mohammed, which the US government brands as a terrorist organisation.
Aref, 35, is an Iraqi-born Kurdish refugee and imam at a mosque in Albany that was raided by the FBI in August 2004.
Hossain, 50, of Yemen, owns an Albany pizzeria. They were to be arraigned on Friday before US magistrate David Homer.
The indictments were based on new evidence presented by prosecutors who, since being sharply criticised by the judge a year ago, have travelled the globe to strengthen their case.
Judge Homer last year said there was no evidence the two men had contact with a terrorist group and released them from jail, saying that the government's case was much weaker than it had first appeared.
Those comments came as civil libertarians and anti-war protesters accused the US authorities of jumping to unfounded conclusions against Muslims since the attacks of 11 September 2001.
US authorities accused of acting
against Muslims since 9/11
The United States has arrested thousands of people on terrorism charges since 9/11 but has seen one high-profile case after another collapse.
In the most recent collapse, the military dropped spy charges this month against Syrian-American airman Ahmad al Halabi, who had faced the death penalty on accusations of aiding and abetting the enemy through espionage at the US prison camp at Guantanamo Bay, Cuba.
In the Albany case, prosecutors assembled a 48-page memorandum documenting Aref's life, including journal entries, taped speeches, phone calls and a poem written by Aref that seems to praise jihad, or holy war.
The government also contends Aref aided the Palestinian group Hamas and fighters linked to attacks on US forces in Iraq.
The new indictments come in addition to 19 previous counts each of money laundering, attempting to provide material support to Jaish-e-Mohammed, and conspiracy charges relating to the FBI sting.
Prosecutors say the two men willingly participated in a plot to launder $50,000 from the sale of a shoulder-fired missile as part of a fake plan to assassinate a Pakistani diplomat.
They have been under house arrest for the past year, wearing electronic monitoring bracelets and only allowed to go to work and the mosque. Federal prosecutors want them jailed pending trial.
Albany is home to nearly 8000 Muslims, some of whom have criticised the arrest of the two men and have refrained from attending mosques for fear of being labelled terrorists.