He was soon sent to Texas and later to Fort Sill in then Indian Territory, where he served as an engineer, supervising the drainage of malaria-infested ponds and the construction of roads and telegraph lines. By 1880, he had worked his way up to the position of quartermaster. Throughout this period, his rise through the ranks was encumbered by racism in the military, though he did have the support of many of the White civilians he encountered, who were impressed by his competency. At one point, he was even brought before a court martial, after money went missing in the post. Realizing that this could be used against him by officers intent on forcing him out of the army, he attempted to hide the discrepancy, which was later discovered. Although he was eventually acquitted, he was found guilty of "conduct unbecoming an officer," and in 1882, given a dishonorable discharge. For the rest of his life, Flipper contested the charges and fought to regain his commission.
After his dismissal, Flipper remained in Texas, working as a civil engineer. He volunteered to serve in the Mexican-American War, but requests to restore his commission we abandoned by Congress. He spent time in Mexico, and on returning to the United States, he served as an informant to Senator Albert Fall on revolutionary politics in that country. When Fall became Secretary of the Interior n 1921, he brought Flipper with him to Washington, D.C to serve as his assistant.
In 1923 Flipper went to work in Venezuala as an engineer in the petroleum industry. Her retired to Atlanta in 1931, and died in 1940. In 1976, Flipper was finally granted a retroactive honorable discharge from the army and a bust of him was unveiled at West Point. Since then, an annual award has been granted to graduating cadets at the Academy who exhibit "leadership, self-discipline, and perseverance in the face of unusual difficulties."
Throughout his life, Flipper was a prolific author, writing about scientific topics, the history of the Southwest, and his own experiences. In The Colored Cadet at West Point (1878) he describes his experiences at the military academy. In the posthumous Negro Frontiersman: The Western Memoirs of Henry O. Flipper (1963), he describes his life in Texas and Arizona after his discharge from the army. .