The move on Friday came in spite of reported objection to the president’s plan within the Pentagon and military.
The president had previously voiced support for the soldiers, including on Twitter.
The three cases of Clint Lorance, Mathew Golsteyn and Edward Gallagher are unrelated.
Two took place in Afghanistan and one in Iraq.
Gallagher was found not-guilty of murder this year, but was convicted of a lesser charge and was demoted.
Trump now restored his previous rank.
Golsteyn is awaiting trial for murder while Lorance is currently serving a 19-year jail sentence for two murders.
Both were granted full pardons.
The New York Times had reported that top officials, including Defense Secretary Mark Esper, were opposed to clearing the soldiers, saying it would undermine justice and serve as a bad example.
Earlier this year, Trump pardoned an army officer who had already served his prison term and was released on parole, following a guilty verdict for a murder in Iraq.
“The President, as Commander-in-Chief, is ultimately responsible for ensuring that the law is enforced and when appropriate, that mercy is granted,” the White House said in a statement.