After the war, he relocated to the Bahamas, where he was courted by Governor Lord Dunmore, who sought to break the monopoly of Panton, Leslie & Co. over the Native fur-trade, and allowed him to return to the Muscogee as an agent of a rival company.

On 16 January 1792, Bowles led a large band of Muscogee warriors who captured and looted the Panton, Leslie, and Co. store in the presidio of San Marcos de Apalache.

While being returned to Spain, Bowles escaped and seized command of a ship to Africa, and eventually made his way back to Florida after stopovers in England and Nassau to regather his British supporters.

Arriving on the Apalachicola Bay in 1799, Bowles made himself "Director General and Commander-In-Chief of the Muskogee Nation", and, on October 31, he issued a proclamation declaring the 1796 treaty between Spain and the United States void because it ignored the Natives' sovereignty over Florida.

He denounced the treaties Alexander McGillivray had negotiated with Spain and the U.S., threatened to declare war against the U.S. unless it returned Muscogee lands that he claimed it had taken illegally, and issued a death sentence against George Washington's Indian agent Benjamin Hawkins.

Bowles had the support of the Seminoles and lower Chattahoochee Creeks because of his generous supply of gunpowder, and of his promises to get more when he captured the Panton-Leslie store at the presidio of San Marcos de Apalache.