In 1777, Malcolm was appointed to command a regiment. Called Malcolm's Additional Continental Regiment, he raised the organization and used his own funds to pay and equip it. He commanded as Colonel, with Aaron Burr as second in command and Lieutenant Colonel, though Burr was often the de facto commander as the result of Malcolm's detached assignments as Deputy Adjutant General or for other duties. Malcolm took part in the battles of Long Island, White Plains, Trenton and Princeton. He was with the Army during the 1777-1778 winter at Valley Forge, and he later commanded Continental forces in upstate New York.