At the outbreak of the War of 1812, Boon joined the Indiana Territorial militia and eventually rose to the rank of colonel.

Two other men briefly competed against Boon for the position, but he defeated them in the general election, 7,397 votes to his closest competitors 3,882.

They offered a premium reward for wolf pelts, Boon capitalized on the new law and earned more than seven-hundred dollars by killing wolves.

[1] Boon's only act of consequence during his short time as governor was to conduct a census of the area purchased by the Treaty of St. Mary's and make recommendations for the creation of counties in the region.

Boon returned to the lieutenant governor's office and remained in that position until January 30, 1824, when he resigned after winning the election to the United States House of Representatives.

He was unsuccessful in his re-election attempt in 1826, defeated by Thomas H. Blake who ran on an internal improvement platform which Boon's party was opposed to.

In Missouri he quickly rose in prominence and became a fierce opponent of Thomas H. Benton and the pro-slavery faction of the state government.