The base remained in a caretaker status until 1909 when the Navy allowed the Marine Corps to establish an Officers’ School of Application at the old naval station on Parris Island, South Carolina. The school on Parris Island was officially opened in 1909.
An effort to set up a recruit depot at Port Royal in November 1910 had to be suspended because of the need for men for an expeditionary force that was organized at that time; but, on 1 June 1911, the recruit depot began operations again, on a three-company basis as a subordinate activity of the Marine Officers' School.

About this time the Navy Department decided to use its property at Port Royal for a disciplinary installation. On 28 August 1911, by General Order No. 122, it changed the designation of the U. S. Naval Station, Port Royal, to the U. S. Naval Disciplinary Barracks, Port Royal, South Carolina. Two days later the Marine Corps turned over its buildings there to the Navy and transferred its activities. The Marine Officers' School, including two companies of the recruit depot, went to Norfolk; the remaining company of recruits continued its training at Charleston, where a one-company recruit depot was operated from this time until June 1912.

Although Marines were assigned to duty at the naval disciplinary barracks at Port Royal, that organization functioned as an installation immediately under the Navy, as distinguished from the Marine Corps; it was not included in the Marine Corps budget. Thus there was no Marine Corps installation at Port Royal from 30 August 1911 until October 1915.

By the latter date the decrease in the number of naval prisoners had greatly reduced the need for the disciplinary barracks at Port Royal, and arrangements were made for the Navy to transfer all its property there to the Marine Corps for use as a recruit depot. The recruit depot had been operating at the Marine Barracks, U. S. Navy Yard, Norfolk, Virginia, since the end of August 1911. In October 1915, the depot was moved from the Marine Officers' School at Norfolk to Port Royal, where, on the 25th, it was established as Marine Barracks, Port Royal, South Carolina. Its commanding officer, Captain Elias R. Beadle, had preceded it by four days. On 28 October the actual transfer of land and buildings from the Navy to the Marine Corps took place, and as of 1 November 1915, for administrative purposes, the U. S. Naval Disciplinary Barracks were attached to Headquarters Detachment, Marine Barracks, Port Royal, South Carolina. From this time forward, the training of Marine recruits was to be the principal mission of this station.