By 1842, the territorial capital had moved from Burlington to Iowa City, where Clarke assisted Governor Lucas with government and political business.

Clarke played a pivotal role in the development of Iowa, helping to define the state's boundaries and forming the first constitutional conventions.

Only four weeks after Clarke delivered his last official message as governor in December 1846, Iowa became the 29th state to join the union.

He became the first president of the Burlington School Board and remained active in local political affairs until tragedy struck in July 1850.

His wife and infant son succumbed to a cholera epidemic that swept through Burlington and other Mississippi River towns.