During the Second Battle of Fort Wagner, he was chief medical officer on Morris Island. In October 1863, he was sent to Florida, and was post surgeon at St. Augustine and Jacksonville; thence he was sent to Virginia, and was with the army when Bermuda Hundred was taken. He was appointed acting staff surgeon, and was stationed three months at Richmond after its fall. For gallant and distinguished services in the field, in 1864 he was brevetted lieutenant colonel of volunteers. Green organized Roanoke Cemetery in 1862, which was one of the first regular burial places for Union Army soldiers.