San Marcos completed shakedown in early May, took on a cargo of landing boats; and, on 19 May, sailed for the Panama Canal and Pearl Harbor.

In January 1946, San Marcos was assigned to Joint Task Force 1 (JTF 1) for Operation Crossroads, the series of atomic tests scheduled for Bikini Atoll during the summer.

Granted provisional radiological clearance, she resumed cargo operations along the west coast in early November; and, by the end of the month, was carrying supplies, boats, and vehicles to the Aleutian Islands.

In December, she put into the Puget Sound Navy Yard at Bremerton; received final clearance in January 1947; and, in the spring, resumed cargo runs between the west coast and the Aleutians.

Recommissioned on 26 January 1951, she completed shakedown in March, was assigned to the Atlantic Fleet's Amphibious Force, and, in May, sailed for the Panama Canal and Little Creek, Virginia.

She arrived at the latter in late May and, soon thereafter, commenced arctic summer resupply operations, under the Military Sea Transportation Service (MSTS), to bases in Canada and Greenland.

In April she departed Norfolk, Virginia, embarked Marines and their equipment at Morehead City, and headed east for her first Mediterranean deployment.

She transited the Straits of Gibraltar in early May and operated with the Sixth Fleet, ranging from the south of France to Benghazi and Phaleron Bay, into October.

During 1953, San Marcos conducted exercises and carried cargo along the east coast and in the Caribbean and underwent overhaul at Boston, Massachusetts.

Winter, spring, and fall of 1954 saw a continuation of those operations including a reserve training cruise, while the summer brought a return to arctic waters for resupply missions.

Severing of diplomatic relations and increased tension between the United States and Cuba and political unrest in the Dominican Republic brought extended operations in the Greater Antilles in early 1961.