Flournoy was a lieutenant colonel in the Georgia Militia and as such became involved in the Florida Patriot War.

[2][3] In 1813, Flournoy replaced James Wilkinson as commander of the Seventh Military District with headquarters in New Orleans.

He managed to alienate important political leaders in New Orleans and Louisiana by questioning their loyalty.

[2] In the fall of 1813, the United States began a coordinated operation to defeat the Red Sticks.

[2] In 1820, he and Andrew Pickens were selected by Secretary of War John C. Calhoun to be United States commissioners negotiating what eventually would be the First Treaty of Indian Springs.

Flournoy immediately resigned, saying that he refused to take responsibility for the actions of others who in the end would not sign the treaty.

In 1801, Flournoy married Sophia Davis of Florida at the house of Governor Milledge of Georgia.