While Zelaya has accepted the plan, Micheletti flatly rejects the reinstatement of the elected head of state.
The State Department said that Honduras, the third-poorest nation in the hemisphere, would continue to receive humanitarian aid, but through channels other than the government in Tegucigalpa.
Despite the end of government-to-government aid, the State Department has yet to formally declare Zelaya's ouster a coup.
Zelaya expressed satisfaction for the moves announced Thursday.
The Micheletti regime finds itself 'ever more alone', Zelaya told a press conference in Washington after his meeting with Clinton.
Micheletti says Zelaya's ouster was not a coup, insisting that the soldiers who dragged him from the presidential palace June 28 were simply enforcing a Supreme Court ban on the president's planned non-binding plebiscite on the idea of revising the constitution.
The Inter-American Commission on Human Rights said last month that the Micheletti government has used excessive force and arbitrary arrests to prevent demonstrations by opponents of the coup.