The following winter he was ordered to Boston, to recruit a regiment of cavalry, of which he was appointed colonel. While the recruiting was going on, a serious mutiny broke out, but the man who, like Cromwell's soldiers, "rejoiced greatly" in the day of battle was entirely capable of meeting this different trial. He shot the ringleader dead, and by the force of his own strong will quelled the outbreak completely and at once.

In May, he went to Virginia with his regiment, where he was engaged in resisting and following Mosby, and the following summer he was opposed to General Early in the neighborhood of Washington. On July 14, when on a reconnoissance his advance guard was surprised, and he met them retreating in wild confusion, with the enemy at their heels. Riding into the midst of the fugitives, Lowell shouted, "Dismount!" The sharp word of command, the presence of the man himself, and the magic of discipline prevailed. The men sprang down, drew up in line, received the enemy, with a heavy fire, and as the assailants wavered, Lowell advanced at once, and saved the day.