The Authority was reorganized and incorporated into the newly formed Florida Department of Transportation (FDOT) in July 1969.

At that time, individual FDOT Districts managed the Turnpike work program, operations, and maintenance in their areas.

In 1990, the Legislature passed Senate Bill 1316, authorizing the expansion of Florida's Turnpike to include construction of non-contiguous road projects as an alternative to assist in meeting the state’s backlog of needed highway facilities.

Jeb Bush signed House Bill 261, creating Florida's Turnpike Enterprise, and directing the Turnpike to pursue innovation and best private-sector business practices, to improve cost-effectiveness and timeliness in project delivery, to increase revenues and expand its capital program, and to improve quality of service to its customers.

It also provides toll collection services for the Garcon Point and Mid-Bay Bridges and the Walter Francis Spence Parkway in Florida's Panhandle.