Yates resigned his commission as commander of the New York National Guard 2nd Brigade in May 1866. He was also the brigade commander of New York City’s First Irish Brigade. In April 1881 New York Supreme Court heard a case involving Yates' daughters and the estate of his first father-in-law, James Rowe. Judge Larremore ruled that Stella and Frances Yates — the daughters from Yates' second marriage — were entitled to the inheritance of their deceased half-sister Catharine, who died in 1874. He died on September 26, 1870 at New York City.