Angered by the invaders and insurrection, townspeople's tempers boiled. Atrocities occurred after local citizens, including town Mayor Fontaine Beckham, were killed during the fighting.

Dangerfield Newby, a former enslaved man fighting to free his family, was the first of Brown’s men killed. A six-inch railroad spike, fired from a musket, severed his neck , and his body was left for roaming hogs. Newby’s ears were sliced off as souvenirs. An enraged citizen swam out in the river and shot Willie Leeman in the head. A similar fate befell William Thompson, killed by a mob and thrown off the railroad bridge into the Potomac, his corpse pelted with bullets throughout the day.

Six were later hanged; five escaped. Osborn Anderson, the only Black man to escape, recounted the events in A Voice from Harpers Ferry (1861).