In 1868, Ames was appointed by Congress to be provisional governor of Mississippi. His command soon extended to the 4th Military District which consisted of Mississippi and Arkansas. Civil unrest was prevalent in the state, one of the last to comply with Reconstruction, but a general election was held during his tenure in 1869 and the legislature convened at the beginning of the following year.
That legislature elected him to the U.S. Senate after the readmission of Mississippi; he served from Feb. 24, 1870 to 10 Jan. 1874 as a Republican. In the Senate, Ames was chairman of the Committee on Enrolled Bills. Upon being elected to the Mississippi governorship, he resigned his seat to assume his duties. He experienced a great deal of resentment from Democratic Party supporters even before taking office in 1874; a riot broke out in Vicksburg in December of 1873 that started a series of reprisals against many Republican supporters. So great was the unrest in following January, the newly sworn-in Governor Ames appealed to the federal government for assistance. That November, Democrats gained firm control of both houses of the legislature. Ames requested the intervention of the U.S. Congress since he believed that the election was full of voter intimidation and fraud. The state legislature, convening in 1876, drew up articles of impeachment against him and all statewide officals. He resigned a few months after the legislature argeed to drop the articles against him.
After leaving office, he headed to first, New York City, then later settled in Lowell, Massachusetts and engaged in the flour producing business (with other business interests on the side). He was appointed brigadier general of volunteers in the Spanish-American War. Several years afterward, he retired from business persuits in Lowell.