In May 1990, VAQ-209 moved to Naval Air Facility Washington and began shifting to the EA-6B Prowler. This improved CVWR-20's electronic attack capability, and also marked the first homeporting of U.S. Navy EA-6Bs outside Naval Air Station Whidbey Island. In 1995, the squadron was deployed for combat operations over Bosnia and participated in Operation Deny Flight and Operation Deliberate Force. From 22 March to 22 September 1995, a two-plane detachment was deployed aboard the aircraft carrier as part of Carrier Air Wing Eight.