After the Civil War fewer troops were stationed at Fort Trumbull, but at least one artillery company continued to serve here each year into the early twentieth century. It became evident during the Civil War that advances in weapons had caused the stone forts built on the seacoast as part of the Third System to become outdated. New guns, called rifled cannon, fired pointed projectiles capable of piercing the stone walls of a fort in a single hit, something that round cannonballs could accomplish only with prolonged bombardment. In addition, rifled cannon could fire from much farther away than earlier guns could, which affected the strategic positioning of forts.
During 1875 and 1876, the army built an installation for a line of heavy guns north of the fort and facing the river in order to enhance the military capability of the post. Known as the North Battery, these gun platforms stood empty until the late 1890s due to funding constraints and changes in military priorities. Meanwhile, the effectiveness of Fort Trumbull continued to decline in the face of further advances in weaponry.
A buildup in arms for Fort Trumbull finally took place in the last decade of the nineteenth century and included three heavy guns called 15-inch Rodmans, which were installed at the North Battery. Most of the other guns were assigned to the older South Battery, the gun line closest to Long Island Sound. For the most part these newly added weapons were already outdated.
During the Spanish-American War (1898), Fort Trumbull served as an embarkation point for troops departing for Cuba or the Philippines.
In 1907, the army downgraded Fort Trumbull to a supply post because three new forts, built on islands at the eastern end of Long Island Sound, were better situated to defend the entrance to the Sound, as well as the approach to New London harbor. A mine company served at Fort Trumbull for three more years, until the post became the Revenue Cutter Service School of Instruction in 1910.