José Francisco Chaves attended schools in St. Louis, Missouri, studied medicine at the New York College of Physicians and Surgeons and engaged in livestock raising in the New Mexico Territory. He married Mary Bowie in 1857, who died in 1874, leaving two children, Lola and Francesca. The former married Mariano Armijo, descendant of a prominent family of Bernalillo county, NM. The latter died in 1895. Chaves served as a soldier in campaigns against the Navajos prior to the Civil War. At the outbreak of the Civil War, Governor Connelly commissioned Chaves as major when the 1st Regiment NM Volunteers for the Union Army formed. After Ceran St. Vrain resigned his commission with the 1st, Kit Carson was appointed colonel and Chaves was promoted to lt-colonel. In 1862 he took part in the Battle of Valverde. He was recognized for gallant and meritorious services, and later helped establish Fort Wingate, of which he was post commander for a long period. He was honorably mustered out of the service of the United States in 1865.
Political career
Returning home he began the study of the law and in due course was admitted to the bar. In politics he was a staunch Republican and in 1858, while absent campaigning against the Navajos, was elected a member of the House of Representatives of the territorial legislative assembly, taking his seat in 1860. In 1865 he was elected delegate from the New Mexico Territory to the U.S. House of Representatives and served in the 39th and 40th Congresses from 1865 to 1867. He was elected back to the House of Representatives in 1868 and successfully contested the election of Charles P. Clever in 1869, serving again until 1871, being unsuccessful for reelection in 1870. In 1875, he was elected a member of the legislative council from Valencia County and was reelected to every succeeding legislature. Chaves was president of the New Mexico Territorial Council for eight sessions. Chaves continued in farming and livestock raising. He was district attorney of the second judicial district from 1875 to 1877 and was a member and president of the New Mexico constitutional convention in 1889. He was New Mexico Superintendent of Public Instruction from 1903 to 1904 and was appointed New Mexico State Historian in 1903, but his career was cut short by an assassination in Pinoswells, New Mexico on November 26, 1904, where he was shot through a window while dining in the home of a friend. He was interred in Santa Fe National Cemetery in Santa Fe, New Mexico. His daughter, Dolores Elizabeth "Lola" Chávez de Armijo, is noted for her successful fight to keep her job as state librarian after Governor William C. McDonald attempted to remove her on the sole basis that she was a woman.