As Florida's fourth governor, Perry helped bring about the settlement of a long-standing boundary dispute with Georgia and encouraged the building of railways in the state.

During the years before the Civil War, Governor Perry foresaw the possibility that Florida might secede from the Union, and in 1858 he urged the reestablishment of the state's militia.

Perry then called for the evacuation of all federal troops from Florida, intending to replace them with the militia.

After his term as governor ended on October 7, 1861, Perry served as colonel of the 7th Florida Infantry Regiment until illness forced his resignation on April 30, 1863.

He retired to his plantation in Rochelle, where he died in March 1865, aged 50 or 51, shortly before the end of the American Civil War.