This marked the first time under the new United States Constitution that the federal government used military force to exert authority over the nation's citizens. It was also one of only two times that a sitting President personally commanded the military in the field; the other was after President James Madison fled the British occupation of Washington, D.C. during the War of 1812.
The military suppression of the Whiskey Rebellion set a precedent that U.S. citizens who wished to change the law had to do so peacefully through constitutional means; otherwise, the government would meet any threats to disturb the status quo with force.
The suppression of the Whiskey Rebellion also had the unintended consequences of encouraging small whiskey producers in Kentucky and Tennessee, which remained outside the sphere of Federal control for many more years. In these frontier areas, they also found good corn-growing country as well as limestone-filtered water and therefore began making whiskey from corn; this corn whiskey developed into Bourbon. Additionally, the rebellion and its suppression helped turn people away from the Federalist Party and toward the Democratic-Republican Party. This is shown in the 1794 Philadelphia congressional election, in which upstart Democratic Republican John Swanwick won a stunning victory over incumbent Federalist Thomas Fitzsimons, carrying 7 of 12 districts and 57% of the vote. The farmers were severely angered.
The hated whiskey tax was repealed in 1803, having been largely unenforceable outside of Western Pennsylvania, and even there never having been collected with much success .