A chapter drawn from her dissertation, which examines amnesty as a tool of governance in the United States during the nineteenth century, this manuscript focuses on the use of amnesty as a response to the Whiskey and Fries’s Rebellions in Pennsylvania in the 1790s. In 1794 and again in 1799, citizens of the new United States violently challenged the role and power of the developing federal government by refusing to pay an excise tax on whiskey and a property tax, respectively. State and federal officials sought to reestablish peace in the rebelling areas without sacrificing authority. Despite scholars’ focus on the use of the militia to accomplish these goals, clemency played a pivotal role in restoring order in 1794 and allowed state and federal officials and communities to negotiate the intricacies of constitutional resistance and federal sovereignty. In 1799, John Adams relied on Washington’s precedent of using military force and charging insurgents with treason before also turning to amnesty, despite fierce resistance from other political elites. Exploring the role of amnesty in the Whiskey and Fries’ Rebellions reveals new perspectives on the development of federal sovereignty, the role of the federal judiciary, and the realities of constitutional politics in the Early American Republic.