After the breakup of the Whig Party in the early 1850s, he briefly joined the American Party before he became a member of the Republican Party. He was a candidate for president at the 1860 Republican National Convention, but Lincoln won the party's nomination. Bates was appointed as attorney general in 1861, at the start of the American Civil War. He successfully carried out some of the administration's early war policies, but he objected to the Emancipation Proclamation and resigned from the Cabinet in 1864 after he had been passed over for a US Supreme Court appointment. After leaving office, he unsuccessfully opposed the adoption of a new state constitution in Missouri.