During the 17th century several Spanish missions were established in the territory of the Apalachee to procure food and labor for the colony at St. Augustine. The largest, Mission San Luis de Apalachee, has been partially reconstructed by the state of Florida. The name "Tallahassee" is a Muskogean Indian word often translated as "old fields" or "old town", and it likely stems from the Creek (later called Seminole) Indians who migrated from Georgia and Alabama to this region in the late 18th and early 19th centuries. They found large areas of cleared land previously occupied by the Apalachee tribe. Earlier, the Mississippian Indians built mounds near Lake Jackson around AD 1200, which survive today in the Lake Jackson Archaeological State Park.

The expedition of Panfilo de Narvaez encountered the Apalachees, although it did not reach the site of Tallahassee. Hernando de Soto and his expedition occupied the Apalachee town of Anhaica in what is now Tallahassee in the winter of 1538-1539. Based on archaeological excavations this site is now known to be located about 0.5 miles (800 m) east of the present Florida State Capitol. The DeSoto encampment is believed to be the first place Christmas was celebrated in the continental United States.