Mount Olympus departed the east coast in early July, arriving Hawaii via the Panama Canal 23 July. With Commander, 3d Amphibious Force, embarked, she was underway from Hawaii 29 August. She arrived Leyte Gulf 20 October, serving as the afloat headquarters for the invasion force. The landing force was subjected to constant air attacks but its survival was assured by the American naval victory in Leyte Gulf, which destroyed the Japanese Navy as an effective combat force.

On 26 October, the flagship departed for Hollandia, New Guinea, via Peleliu, in preparation for the next assault on the Japanese‑occupied Philippines. After invasion rehearsals in Huon Gulf, New Guinea, the ship departed Manus Island, Admiralties, 31 December for the assault on Lingayen 9 January 1945. After the initial assault and with the ground force commander disembarked, Mount Olympus was underway 11 January from Lingayen. She called at Ulithi to allow Commander, 3d Amphibious Force, to disembark to travel by plane to Hawaii, while she herself sailed for overhaul at San Francisco, arriving 11 February and leaving 22 April for Hawaii and Guam.