While anchored off Green Cay, she was officially commissioned into the Confederate States Navy as CSS Florida on August 17, with Lieutenant John Newland Maffitt in command.

Having resupplied her stores armed with the gun accessories she lacked, along with added crew members, Florida escaped to sea on January 16, 1863 under (now) Captain John Newland Maffitt.

[3] After coaling at Nassau, she spent six months off the coasts of North and South America and in the West Indies, with calls at neutral ports, all the while making captures and eluding the large Federal squadron pursuing her.

She then skirted the U.S. coast, sailed east across the Atlantic Ocean to Tenerife in the Canary Islands and thence back southwest to Bahia, Brazil, arriving on October 4, 1864.

Anchored at Bahia on October 7, Florida, while her captain was ashore with half his crew, was caught defenseless in an illegal night attack by Commander Napoleon Collins, of the U.S. Navy steam sloop-of-war USS Wachusett.

Commander Collins was court-martialed and was convicted of violating Brazilian territorial rights, but the verdict was set aside by United States Secretary of the Navy Gideon Welles.

At Newport News, Virginia, on November 28, 1864, Florida reached the end of her career when she sank under dubious circumstances after a collision with the United States Army Transport USAT Alliance, a troop ferry.