"Amphitrite" carried out her gunnery training until departing New Bedford on 5 October for the Boston Navy Yard, where she underwent repairs from 7 October-14 November. Receiving drafts of men for gunnery class at Tompkinsville and Norfolk, the monitor proceeded back to Port Royal, arriving there on 29 November. Outside a brief port visit to Brunswick, Ga., from 28 January-6 February 1901, "Amphitrite" remained at Port Royal until 10 May, when she sailed for Norfolk and Tompkinsville, arriving at the latter on 3 June, en route back to her ultimate destination of New Bedford. "Amphitrite" continued the important work of training gun captains through the summer and into the fall. Deemed in need of a general overhaul, "Amphitrite" was placed out of commission at the Boston Navy Yard on 30 November 1901.