"Philadelphia" remained in the Samoan Islands until 21 May 1899, when she steamed for the west coast via Honolulu. "Philadelphia" served as flagship of the Pacific Station until 6 February 1900, when Rear Admiral Kautz transferred his flag to . The cruiser continued Pacific operations until 1902, conducting training cruises, drills, target practice, and port visits. Returning from a six-month cruise off the Panamanian coast, "Philadelphia" arrived San Francisco 17 July 1902. Needing extensive repairs, she was ordered to the Puget Sound Navy Yard for decommissioning. Arriving Bremerton, Washington 23 August, she decommissioned at Puget Sound 22 September 1902. "Philadelphia" was housed over and became a receiving ship at Puget Sound Navy Yard 12 May 1904. She continued this service until 4 November 1912, when she became a prison ship. Resuming service as a receiving ship 10 January 1916, she was redesignated with the hull number IX-24 (unclassified miscellaneous) on 17 July 1920. She was struck from the Navy List on 24 November 1926. Cruiser "Philadelphia" was sold at public auction at the Puget Sound Navy Yard in 1927 to Louis Rotherberg.