Following his career as a judge, James Duane Doty served as a member of the Michigan Territorial Council from 1834 to 1835, representing the western part of the territory. In this capacity Doty argued for the creation of a new territorial government for Wisconsin, sending petitions to Congress in favor of splitting Michigan Territory into two parts, one east and one west of Lake Michigan. Doty had supported this idea as early as 1824, and argued that the growing number of residents in Wisconsin were not adequately provided for by the territorial government in Detroit, which was hundreds of miles away from any settlement in Wisconsin. Doty claimed that votes sent by residents west of Lake Michigan could not be sent to Detroit in time to be counted, and that the residents in Lower Michigan cared little about the affairs west of the lake. In 1835, his wishes were partially granted when the Governor of Michigan Territory created a separate legislature to govern the western part of the territory as Michigan prepared for statehood. In 1835, Doty campaigned to represent western Michigan Territory as a delegate in Congress, but he lost in a three way election to George W. Jones. Both Doty and Jones were running as Democrats, but Doty had little true loyalty to any political party. He was conservative in view and usually aligned himself with whichever people were most popular at any given time. After losing the election, James Doty turned to land speculation and bought thousands of acres of land across the state, some of which he began developing into the city of Madison, Wisconsin.

In 1836, Wisconsin Territory was officially created. James Doty hoped to be the territorial governor, but President Andrew Jackson appointed Henry Dodge, Doty’s longtime political rival, to the post. With no public title, Doty worked to improve his land holdings in what would become the city of Madison. Doty had this land surveyed and platted, and made plans to create a city on the isthmus between lakes Mendota and Monona. To gain recognition for the planned city, Doty lobbied the new territorial legislature to select his proposed city as the capital of Wisconsin. A temporary capital had already been established at Belmont, Wisconsin, but its distance from Milwaukee and Green Bay coupled with the dissatisfaction of many legislators towards the facilities at Belmont made it likely that the capital would be moved. Doty used numerous tactics to ensure that Madison would be made capital city, wooing legislators with plans for canals and railroads and offering legislators who voted to make Madison the capital choice lots in the new city. Madison was declared permanent capital in November, 1836, and construction at the new city began in 1837. In 1838, Doty was elected as Wisconsin Territory’s congressional delegate, defeating George W. Jones in a rematch of the 1835 election. Despite being elected as a Democrat, Doty formed personal friendships with several Whigs in Washington, D.C., including Henry Clay. In 1840, Whig Party candidate William Henry Harrison was elected president, and he made plans to appoint Doty to the governorship of Wisconsin Territory despite Doty’s status as a Democrat. Harrison died before he could make the appointment, but vice president John Tyler fulfilled Harrison’s desire after ascending to the presidency in 1841. James Doty was largely unsuccessful as territorial governor, the Dodge supporters in the territorial legislature rejected most of the legislation Doty supported, and Doty failed on four separate occasions to get public support for Wisconsin statehood. Doty’s term ended in 1844, and he was not reappointed by Tyler, who instead selected Nathaniel P. Tallmadge to the post. This left Doty to once again return to his private life.

In 1846, James Doty returned to politics, this time as a delegate to the First Wisconsin Constitutional Convention. Doty came to the convention as an independent, but sided with the Whigs on most issues and emerged as the opposition leader at the convention, which had a clear Democratic majority. After much debate, the convention produced a constitution, but the state’s residents considered the document to be too radical and voted it down in a referendum, despite public campaigns for the constitution led by Doty and other delegates. A second convention called in late 1847 produced a constitution that was accepted by the people, and this enabled Wisconsin to achieve statehood in 1848. Doty was elected to the United States House of Representatives shortly after Wisconsin became a state, and served from 1849 to 1853 as the representative of Wisconsin’s newly created 3rd congressional district and served as part of the 31st and 32nd Congresses. He was replaced by John B. Macy. After leaving Congress, Doty left public life and retired to his home on an island (now named Doty Island) between Neenah and Menasha, Wisconsin. His log-cabin home, relocated from the east end of the island, is located in Doty Park on the southeastern riverfront of Doty Island (on the island’s Neenah side). It is listed on the National Register of Historic Places.

In 1861, James Doty returned to public service when Republican President Abraham Lincoln appointed him to the position of Superintendent of Indian Affairs for Utah Territory. Doty was successful in this position. In 1863, Stephen Selwyn Harding, Utah’s territorial governor, was removed from office after public backlash from his criticism of the LDS Church and the practice of polygamy. Lincoln appointed Doty to the governorship shortly thereafter. As governor, Doty was able to repair the relationship between the federal government and the territory’s Mormons. Doty also promoted the construction of schools and negotiations with local Native American tribes. James Doty died in office on June 13, 1865, shortly after the outbreak of Utah’s Black Hawk War. He was buried at the Fort Douglas Cemetery in Salt Lake City, Utah.