Upon arriving in Charleston, Howe acted as an adjutant to Major General Charles Lee, who had been appointed Commander of the Southern Department of the Continental Army. Howe directly commanded the South Carolina militia during the First Siege of Charleston in June 1776 and was assigned command over the defenses of the city proper. Lee was recalled to the North to assist General George Washington, and in his absence, James Moore was appointed Commander of the Southern Department. Howe was left in command of Charleston and Savannah, Georgia in Lee's absence, and in September 1776, he became embroiled in a controversy involving the provincial assembly of South Carolina allowing its officers to recruit soldiers from North Carolina's continental line units. Howe pleaded with the Provincial Congress of North Carolina to allow South Carolina to recruit within the former state's borders because of the greater number of white males in that state. Eventually, North Carolina acceded to that request but only after ordering Howe to reclaim the North Carolinians who had already been lured away by the South Carolinians. The South Carolina Council took offense and demanded that Howe pay the recruitment bonuses for the men if he wished to have them back. With James Moore's death on April 15, 1777, Howe assumed command of the Southern Department.