On August 24, the Stars and Stripes captured the British ship Mary Elizabeth attempting to run into Wilmington with a cargo of salt and fruit.
After that, the ship went to Philadelphia for repairs and was decommissioned September 14, though quickly repaired and back in service. On September 29, the Stars and Stripes was assigned to the East Gulf Blockading Squadron where she remained for the rest of the war. This is when she had the encounters with the CSS Spray and the St. Marks area.
In 1863, she captured the sloop Florida in St. Marks Bay with a cargo of cotton and tar. on June 3. Then, its boats along with those of the USS Somerset went to Marsh Island, Florida to destroy saltworks. Later she destroyed the blockade runner schooner Caroline Gertrude aground at the mouth of the Ochlockonee River December 29.