In January 1861,
Florida became the third state to secede from the Union. At this time, the pro-secession Winder was in command of the defenses in
Pensacola, which included
Fort Pickens. However, he was away on leave and so Lt.
Adam J. Slemmer took command and prevented the fort from falling into rebel hands. The Union would retain control of the fort for the rest of the war. Winder resigned his U.S. Army commission on April 20, 1861, and offered his services to the state of North Carolina. He was appointed a
colonel in the
Confederate Army infantry on May 21. He was then promoted to
brigadier general on June 21 and the next day was made Assistant
Inspector General of the Camps of Instruction that were in the Confederacy's capital of
Richmond, Virginia, a post he would hold until October 21. Winder designated Samuel B. Maccubbin chief of detectives and gave him a force of
Plug Uglies imported from Baltimore to police the population of Richmond. Winder's first order was established
prohibition of alcohol and required all citizens to surrender their firearms. Even though there were daily accusations or entrapment and corruption against his "plug-ugly" police force, Winder refused to order an investigation. By October 1864 newspapers reported the crime rate in Richmond exceeded the worst days of Baltimore or New York and much of the blame went to the corrupt police force. This earned him the moniker "The Dictator of Richmond". In addition to his duties involving prisons, he was responsible for dealing with
deserters, local law enforcement, and for a short time setting the commodity prices for the residents of a city dealing with a doubled population. During this time, he commanded
Libby Prison in Richmond as well. In April 1864, Winder appointed Captain
Henry Wirz commandant of a new prison camp in Georgia called Camp Sumter, better known as the infamous
Andersonville Prison. Winder commanded the Department of
Henrico for much of the war, until May 5, 1864. He then commanded the 2nd District of the Department of North Carolina & Southern Virginia from May 25 until June 7. During the war, Winder was frequently derided in
Northern newspapers, which accused him of intentionally starving Union prisoners. Military historian
Ezra J. Warner believes these charges were without merit, saying, "Winder adopted every means at his command to assure that the prisoners received the same ration as did Confederate soldiers in the field, scanty as that allotment was." McElroy claims that on July 27, 1864, Winder issued an order that if Union troops (under
General Stoneman) were to come within seven miles of Andersonville, the guards were to "open upon the Stockade [i.e. upon the prisoners] with grapeshot, without reference to the situation beyond these lines of defense". ==Death and legacy==