It's Donegan's second time in a Middle East staff position, after serving as director of operations for CENTCOM before his most recent position as the aide to the deputy chief of naval operations for operations, plans and strategy.
"For our friends and partners here in the region, our presence here far from home is a constant and visible assurance that our country takes its commitments seriously and that we are here to stay," Donegan said at the ceremony.
His change of command was a long time coming. Miller had been nominated in March 2014 to take over as chief of naval operations for operations, plans and strategy, but Donegan's nomination to replace him in Bahrain was held up by an investigation into whether he had a role in the far-reaching "Fat Leonard" bribery scandal, an official told Defense News earlier this year.
He has clocked more than 3,800 hours in 30-plus types of aircraft, including 800 traps on 15 different carriers, according to his official bio.
Donegan is also a graduate of U.S. Navy Test Pilot School, Navy Fighter Weapons School, Navy Nuclear Power School, the Air Force Command and Staff College, the Joint Forces Staff College and the Harvard Kennedy School of Government's executive education program.
His awards include Defense Superior Service Medal, five Legions of Merit, the Defense Meritorious Service Medal, four Meritorious Service Medals, the Air Medal, two Navy Commendation Medals and two Navy Achievement Medals.
Meghann Myers is the Pentagon bureau chief at Military Times. She covers operations, policy, personnel, leadership and other issues affecting service members. Follow on Twitter @Meghann_MT