At the end of his university studies in 1823, he opposed a military pronunciamiento which was then underway and menacing the constitutional assembly of the Republic of Central America then in progress. In 1836 he was a member of the legislature of Nicaragua, and in 1838 he was a member of the Nicaraguan constitutional assembly, and helped to establish the University of Granada. In 1843, when a confederation of Honduras, Nicaragua, and El Salvador was founded, Chamorro was a member of its Executive Power and avoided a war with Guatemala. In 1845 he was governor of Nicaragua and in 1846 minister of finance. He returned to the second post in 1851 but was forced to resign when he suggested a cut in the military budget.
In 1853 he was head of the Executive Power in Nicaragua; when faced with a revolt, he was besieged in Granada for 221 days. The Conservatives were finally ousted from power with the help of the U.S. soldier of fortune William Walker.