Naval Base Subic Bay following the eruption of Mount Pinatubo, operated with the INTERFET peacekeeping taskforce, participated in Pacific Partnership deployments, and provided assistance following the massive floods in Pakistan in 2010.

Following the 17 October 1989 Loma Prieta earthquake, Peleliu was one of the 24 U.S. Navy and Military Sealift Command ships that rendered assistance.

Peleliu returned home to Naval Station Long Beach in July and later that summer entered the shipyard for an availability period that was scheduled to last nearly a year.

The U.S. response to the Iraqi invasion of Kuwait in August 1990 curtailed the shipyard availability and forced Peleliu into an accelerated schedule of pre-deployment training, but she did not deploy for Operation Desert Shield/Desert Storm.

In June 1991, while en route to the Persian Gulf, she was diverted from a scheduled port call in Hong Kong to the Philippines, where she participated in the evacuation of the Americans from the Naval Base Subic Bay following the volcanic eruption of Mount Pinatubo.

This eruption was one of the largest of the past 100 years and covered a large region of the Philippines in volcanic ash and caused extensive damage to American military bases in the area, including Naval Station Subic Bay, Naval Air Station Cubi Point, and Clark Air Force Base.

[citation needed] Peleliu was deployed to East Timor as part of the Australian-led INTERFET peacekeeping task force from 26 October to 27 November 1999.

[5] Peleliu departed from San Diego in August 2001 with the 15th Marine Expeditionary Unit on board for a six-month deployment in the Western Pacific.

[6] While on deployment in support of Operation Iraqi Freedom, in 2004, and as flagship of Expeditionary Strike Group One, a hostile boat was intercepted by warships at sea in the Indian Ocean, and 15 people were detained.

An estimated 2,800 pounds (1,300 kg) of hashish was seized by American and Australian warships after the interception of the boat in the North Arabian Sea.

The medical personnel on board Peleliu included teams from the U.S. Navy and ten other countries, and also from three private assistance organizations.

On 10 August 2008, Peleliu responded to a distress call from a merchant ship, Gem of Kilakari, that was being attacked by armed pirates in the Gulf of Aden.

[11] On 24 November 2010, Peleliu returned full circle and she was berthed in the Subic Bay Freeport Zone on her first visit there since the evacuation by the Navy in 1991.

The ship visited numerous ports including, Apra Harbor, Guam; Sasebo and Okinawa, Japan; Subic Bay, Philippines and Singapore.

Upon return, the ship made preparations to decommission in March 2015 after 34 years of service, 17 deployments and more than 1.6 million kilometres (990,000 miles) transited.

[17] Peleliu was struck April 30, 2024 and sits moored at NAVSEA Inactive Ships On-site Maintenance Office, Pearl Harbor, Hawaii pending final disposal.