The Holy Land Foundation for Relief and Development shut down seven years ago.
Linda Moreno, the lawyer for Ghassan Elashi, a former chairman of the group, said "the evidence is clearly going to show you that their mission was charitable".
"Holy Land's mission was not political."
Elashi and Shukri Abu Baker, Holy Land's former chief executive, are again each charged with conspiracy, supporting a foreign terrorist organisation, money-laundering and filing false tax returns.
Prosecutors had already dropped most of nearly 30 counts against Mufid Abdulqader and Abdulrahman Odeh.
The men will still each face three conspiracy charges.
Mohammed El-Mezain, a former Holy Land chairman acquitted on most charges in the first trial, is charged with one conspiracy count.
The first trial ended in October 2007 with one man acquitted on 31 charges but jurors unable to agree on verdicts for others.
The defence says the government admitted it listened to the telephone conversations of the suspects over a 10 year-period but gathered little direct evidence related to the prosecution.
Prosecutors have said Holy Land had existed to support Hamas, raising money to support schools and community organisations run by or on behalf of the Palestinian movement, which now controls the Gaza Strip.
Defence lawyers told the jury that none of the charities Holy Land supported have been designated as terrorist groups by the US government.
About two dozen family members of Holy Land defendants and supporters gathered outside the Dallas courthouse, as they often did during last year's trial, and condemned prosecutors for going after the defunct charity.