The tracks and junction were rebuilt after the war, but the railroad defaulted on its payments to the Florida Internal Improvement Fund.

The P&G then built from Tallahassee west to four miles (6 km) short of Quincy, stopping in 1863 in the middle of the American Civil War.

After renaming the FA&GC the Florida Central Railroad, set his carpetbagger protégé, Milton S. Littlefield, a former Union general known as the "Prince of Carpetbaggers", loose in Tallahassee to buy, cheat, and otherwise defraud Florida legislators in order to obtain a new charter for a railroad that Littlefield promised would be extended west from Quincy to Pensacola.

[4]: 101  Littlefield and Swepson then launched a major swindle, personally enriching themselves from the sales of company bonds to unwitting investors.

[4]: 101–102  Due to the embezzling of such funds, the company was unable to extend the line to Pensacola, reaching only an additional 20 miles to Chattahoochee instead.

[5] The Tallahassee Subdivision was notably used by the Seaboard Air Line for passenger service from Jacksonville to New Orleans, which was operated jointly with the Louisville and Nashville Railroad.

The Tallahassee Subdivision crossed or connected with ACL branch lines in Jacksonville, Mattox, Live Oak, Drifton, and Chattahoochee.

[2]: 12 The Gulf Wind continued to operate on the Tallahassee Subdivision under the Seaboard Coast Line until 1971, when passenger service was taken over by Amtrak.