In 1875, he was serving on USRC Active, homeported at New Bedford, Massachusetts until he was assigned the duties of assistant inspector of the U.S. Life-Saving Service at New York City.

[6][Note 2] In 1876 he was appointed assistant inspector of the Third Life Saving District of the U.S. Life-Saving Service and while serving in that billet was promoted to first lieutenant on 25 March 1878.

[4][5] In 1878, Shoemaker was transferred to the office of Sumner I. Kimball, then the Chief of the Revenue Marine Bureau and was assigned investigating duties and heard complaints against keepers at all Life-Saving Service stations.

[8] Shoemaker was assigned as executive officer on the USRC Seward in 1882 which at the time patrolled the Gulf Coast and was homeported at Bay Saint Louis, Mississippi.

[5] During this assignment, he located and obtained sites for stations, conducted 300 investigations and brought serious charges against four assistant superintendents of the service.

[3][5][9] On 19 March 1895, Secretary of the Treasury, John Griffin Carlisle appointed Shoemaker to replace Leonard G. Shepard as Chief of the Revenue Cutter Division and promoted him to senior captain.

Lyman Gage, who succeeded Carlisle as Secretary of the Treasury, called for enlisted men injured in the line of duty to be included on a pension list; Shoemaker endorsed this reform also.

[10] Congress didn't take action on legislation allowing this to occur until the Overland Relief Expedition of 1897–1898 and the Spanish–American War brought public attention to the Revenue Cutter Service.

[15] During his tenure, Shoemaker acquired the land for Chase to use as a homeport and for repairs at Arundel Cove in Curtis Bay, Maryland.

[16] This site eventually became the service's vessel construction and overhaul facility and today is known as the United States Coast Guard Yard.