Manoora was initially converted into an armed merchant cruiser (AMC), operating primarily in Australian, New Guinea, and Pacific waters, with deployments to Singapore and the Bay of Bengal.

After the war's end, the ship was used to transport occupation forces and refugees until 1947, when she was decommissioned from naval service and returned to the Adelaide Steamship Company.

[7][4] On 12 June, shortly after Italy became involved in the war, Manoora intercepted the Italian passenger vessel Romolo, which was scuttled off the Solomon Islands.

[7] Between the end of 1940 and September 1941, Manoora's operated around the north and east coasts of Australia, around New Guinea and New Britain, and to the Solomons, Nauru, and Ocean Island.

[3] The ship was recommissioned on 2 February 1943 with the pennant number C77, and after spending six months on amphibious warfare training in Port Phillip, was deployed to New Guinea.

[7] At the start of 1945, the ship participated in operations at Lingayen Gulf, followed by the Borneo campaign, with landings at Tarakan on 1 May, Brunei Bay during 9 and 10 June, then Balikpapan on 1 July.

[7] After the war's end, Manoora was used to transport the soldiers and equipment of occupation forces, and return evacuees from the East Indies region to their homes.

[10][11] In 1947, Minister for Immigration Arthur Calwell requested the use of Manoora to help Australian and British citizens escape the increasing unrest in India preceding the nation's independence and resettle them in Australia.

[12] Plans were made for multiple voyages from India to Australia, although only one sailing eventuated, arriving back in Fremantle on 15 August: austere accommodations on the barrack decks prompted many potential passengers to instead wait for commercial vessels.

[12] After two years of maintenance and refit at Cockatoo Island Dockyard to remove the wartime modifications, Manoora was returned to the Adelaide Steamship Company on 31 August 1949.