He moved north into the Wisconsin Territory in 1841, to work as the assistant secretary of the territory under Alexander Pope Field, in Madison.[3][4] While living there, he also worked as a law partner to Field, and became active in politics. He was a candidate for delegate to Wisconsin's first constitutional convention in 1846, but was defeated by John Y. Smith. After the first constitution was rejected by voters, however, he was elected to serve in the 5th Wisconsin Territorial Assembly as a representative of Dane, Green, and Sauk counties.[2] This was the last session of the territorial government before the adoption of Wisconsin's second constitution and their admission as a U.S. state.
In the 1848 fall general election, Botkin was elected to a two-year term in the Wisconsin Senate running on the Whig Party ticket. He represented Dane County in the 2nd and 3rd legislatures. During the 1849 session, he was the Whig nominee for United States Senator, but the Democrats held a substantial majority in the Legislature and selected Isaac P. Walker instead. He ran for re-election in 1850, but was defeated.[4] After leaving the Senate, he was elected to a one-year term in the Wisconsin State Assembly for the 5th Wisconsin Legislature.[2][5]