Along with RFA Fort Victoria, the ship was equipped with two Phalanx CIWS point defence guns during a refit at Tyne in 1999.

In March 2000, the ship was equipped with five Westland Sea King helicopters and sent to Mozambique to help with disaster relief work following devastating floods.

In May she accompanied the aircraft carrier HMS Illustrious to Sierra Leone to support British operations to restore stability to that country.

Late in the year, during a deployment in the Mediterranean, the ship helped passengers of the Greek ferry Express Samina which had run aground and sunk during a storm on 26 September.

In September 2009, Fort George, whilst working with the Type 23 frigate HMS Iron Duke, was involved in the largest ever drugs seizure to date by the Royal Navy, when 5.5 tonnes of cocaine were seized from a converted fishing vessel MV Cristal in the Atlantic Ocean off South America.