1990–1999

Chatham joined Operation Sharp Guard to enforce the embargo against the former Yugoslavia in 1993. Her most notable action was on 1 May 1994 and the capture of the Maltese freighter Lido II, which was suspected of smuggling fuel to Montenegro. The British frigate assisted the Dutch frigate HNLMS Van Kinsbergen, who had forced the merchant to stop.

Three Yugoslav Končar-class missile boats challenged the NATO operation and one of them attempted to ram Chatham. The corvettes were driven off by the actions of the British warship, supported by Italian Tornado aircraft which scrambled from an airbase at Gioia Del Colle. Lido II underwent repairs after sabotage to the ship's engine room by her crew, before being diverted to Italy. The leaking was contained by an engineering party from Chatham. Seven Yugoslav stowaways were found on board.^[4][5]

Under the command of Captain Christopher Clayton, she was guardship to the royal yacht HMY Britannia during the withdrawal from Hong Kong in 1997^[3] (and served as the control military operations in the months prior to the handover).

2000–2009

In May 2000, Chatham was part of the Amphibious Ready Group (ARG) sent to the coast of Sierra Leone to oversee the evacuation of British, EU and Commonwealth nationals as part of Operation Palliser, under the captaincy of George Zambellas.

In March 2003, Chatham became the first British warship to fire her guns in anger since the Falklands War, when, as part of Operation Telic, she engaged targets on the Al-Faw Peninsula of southern Iraq. Approximately 60 rounds were fired at a variety of targets from her 4.5-inch gun. In company with HMS Marlborough, HMS Richmond and HMAS Anzac she remained on station for the following 72 hours at immediate readiness to provide fire support to the troops of the Royal Marines as they advanced up the peninsula.

Chatham deployed from the UK to the Persian Gulf in January and returned in August. During the deployment, in the run-up to and the conduct of the invasion of Iraq, the ship spent around 90 days at sea continuously at defence watches in the northern part of the Persian Gulf. At times she came very close to hitting mines laid by Iraqi dhows and tugs in the shallow waters to be found in the area.

Chatham hosted filmmaker Chris Terrill of the BBC for the television programme Shipmates which charted the life of sailors in the Royal Navy. In the program, he filmed Chatham on active service in the Persian Gulf, whilst on an anti-terrorist mission. The show also covered the Chatham's humanitarian relief efforts off the coast of Sri Lanka after the December 2004 Indian Ocean Tsunami.^[6]

On 18 April 2005, Chatham sent a party ashore at Alexandria in Egypt to provide a burial for the recently uncovered remains of thirty British sailors and officers who had died during or after the 1798 Battle of the Nile.^[7]

On 31 October 2006, she visited the town of Chatham, Massachusetts, on her way to Boston.

In 2008, Chatham was responsible for the capture of six tonnes of the 23-tonne narcotic haul seized by the Royal Navy between January and August 2008. As of March 2010, she was the NATO flagship for international naval operations against Somali piracy.^[8]

2010–2011

On 17 May 2010, Chatham destroyed two pirate boats in the Somali Basin, forcing the pirates to return in the mother ship to Somalia.^[8]

On 20 May 2010 Cyclone Bandu disabled a cargo vessel, MV Dubai Moon, and left her drifting off the Somali coast. Before the cargo vessel sank, 23 crew members were rescued by helicopters from Chatham.^[9]