During the American Civil War, Baker served as colonel of the 10th Minnesota Volunteer Infantry in the Union Army in 1862–1863.[2] He was appointed Provost Marshal for the Department of Missouri, and served till the close of the war.[1] He was mustered out of the volunteers on October 21, 1865.[2] In recognition of Baker's service, on January 13, 1866, PresidentAndrew Johnson nominated Baker for appointment to the grade of brevetbrigadier general to rank from March 13, 1865, and the U.S. Senate confirmed the appointment on March 12, 1866.[3]
After the war, Baker was appointed Register of Public Lands at the Boonville, MissouriFederal Land Office, which he performed for two years. He then retired to a farm in Minnesota, and was appointed Commissioner of Pensions by President Grant from 1871 to 1875.[1]
Together with Judge Lorin Cray, Baker paid for the creation of a four-ton granite marker known as the "Hanging Monument", commemorating the mass execution of 38 Dakota men in Mankato on December 26, 1862. [4] Erected in 1912, it soon became the object of controversy and was finally removed by the City of Mankato in 1971.[4]
Baker died at Mankato, Minnesota, May 25, 1913.[5] He is buried at Glenwood Cemetery in Mankato.[2]