Haller fought Seminole Indians in Florida in 1840–1841 and later served with distinction at Monterrey, Veracruz, and other battles during the Mexican–American War, officering in the same regiment as Ulysses S. Grant. He distinguished himself in the Battle of Churubusco, where he took a key part in the assault on Molino del Rey. In 1852, the Army promoted Haller to major and transferred him in 1853 to Washington Territory, stationed at Fort Dalles, Oregon with U.S. 4th Infantry units. He took part in the Northwest Indian wars of 1855-56 and the San Juan Islands' Pig War border crisis between the United States and Great Britain in 1859.