After he returned from the War, he ran for Governor of Montana in 1948, winning the Democratic primary and advancing to the general election, where he defeated incumbent Republican Governor Sam C. Ford by a wide margin. Bonner ran for re-election in 1952, and he was narrowly defeated by State Senator J. Hugo Aronson. He ran for Governor again in 1956, but lost the Democratic primary to Arnold Olsen, who ended up losing to Aronson in the general election. In 1960, when United States Senator James E. Murray opted not to run for re-election, Bonner ran to succeed him, but, in a crowded primary, was defeated by Congressman Lee Metcalf, who would go on to serve in the United States Senate for three terms. From 1968 until his death, he served as an associate justice of the Montana Supreme Court.
