After his appointment as a colonel in 1776, Eaton was elected to the North Carolina Council of State, an executive body elected by the North Carolina General Assembly which assisted the governor in managing the state's affairs. Eaton served under Richard Caswell in that governor's terms as first and fifth governor of the post-Revolution state, and was re-elected to the Council in 1779 and 1784. In between his terms as a councillor, Eaton served with the militia in the southern theater against the British Army and its local Loyalist tributaries, but was primarily a politician, and had less military experience than many of his colleagues.