He was defeated for re-election in 1858 by a narrow majority of 3000 votes even though the New York gang the Dead Rabbits combed the city's cemeteries for names to add to the voter rolls. The Bowery Boys and their allies the Atlantic Guards poured into Bayard Street to engage in the most desperate and largest free-for-all in the city's history. Fifty-two policemen were injured in the New York City Police Riot.
Following his service as mayor Wood returned to the United States Congress. In 1854 he was elected Mayor of New York City. Reelected in 1860 after an electoral loss in 1857 by a narrow majority of 3000 votes Wood evinced support for the Confederate States of America during the American Civil War suggesting to the New York City Council that New York City secede from the Union and declare itself a free city in order to continue its profitable cotton trade with the Confederacy.