Boente, a 33-year veteran of the Justice Department, was tapped earlier this year to serve as acting attorney general after Sally Yates was fired. He went on to serve as acting deputy attorney general.
He is serving as acting assistant attorney general of the National Security Division and will remain in that post until John C. Demers, an attorney for Boeing who worked at the Justice Department under President George W. Bush, is confirmed.
"Dana is a superb prosecutor — tough, smart, honest, compassionate and fair — and a cherished colleague and friend," said Chuck Rosenberg, a former U.S. attorney for the same district who recently resigned as acting head of the Drug Enforcement Administration.
Boente submitted his resignation Thursday, and Trump has not named a successor for him in Virginia. Sens. Mark R. Warner and Tim Kaine, both Virginia Democrats, said in a statement Friday afternoon that they are accepting applications for the position.
"We are grateful for Dana Boente's public service and look forward to reviewing qualified candidates and selecting the right individual for this significant role," they said.
The job is an important and high-profile one. The Eastern District is home to the CIA and the Pentagon, and its prosecutors often handle terrorism cases. It includes about 300 lawyers and other employees with offices in Alexandria, Richmond, Norfolk and Newport News.
A native of Illinois, Boente is known for his mild manner and intense devotion to his work. He is in the office most weekends and tends to eat a microwaved lunch at his desk.
"Dana is an incredibly hard-working prosecutor who has dedicated his career to this district," said Geremy Kamens, the federal public defender for Alexandria. "He's been an able and professional leader at the U.S. attorney's office, and he'll be missed."
Boente oversaw the prosecution of former Virginia governor Robert F. McDonnell (R), whose conviction was ultimately overturned by the Supreme Court, and former congressman William J. Jefferson (D-La.), whose conviction was partially overturned after that ruling. His office has assisted in the probes of Hillary Clinton's emails and possible coordination between the Kremlin and the Trump campaign.
Boente previously worked in the tax division and as an interim attorney in the Eastern District of Virginia and the Eastern District of Louisiana.
Matt Zapotosky contributed to this report.