U.S. ground troops never reached San Juan during the actual fighting on the island, as the peace agreement was reached before they could get there from the south. However, the U.S. government of Puerto Rico, which began with the military government in Ponce, moved and established its center at San Juan, and Charles H. Allen, the first civilian governor, was inaugurated there in 1900.

San Juan, the capital and major northern city of Puerto Rico, was the site of the first armed conflict between the United States and Spain on the island. On May 10, the U.S.S. Yosemite exchanged fire with the fortress of San Cristobal on the shore in San Juan. For the next few days, ships commanded by Rear Admiral Sampson also bombarded the city, causing scattered damage.