The USN, the United States Marine Corps (USMC), the Ministry of Interior, and others run the security at the airfield.

Often referred to as the nearby city of Manama, Muharraq Airfield was the last stop for most US troops being sent to fight in the War in Afghanistan (2001-2021), including with the multinational International Security Assistance Force.

From 15 September 1967 to 8 August 1969 Air Forces Gulf Communication Squadron RAF flew from the base.

101 Squadron RAF during the Gulf War training with Royal Air Force Panavia Tornado GR1's.

The base is also used by Mine countermeasures helicopters patrolling the Persian Gulf such as HM-15's Sikorsky MH-53E Sea Dragon's.