Most of the Apalachees who were not killed outright or enslaved during the English attacks moved north into British territory. A small number relocated with the Spaniards around St. Augustine. The Apalachees from Mission San Luis had become disenchanted with their Spanish allies and moved to French-occupied Mobile at the invitation of Jean Baptiste Le Moyne de Bienville. French accounts of the Apalachees in Mobile describe them as being good Catholics who insisted on being furnished with a priest. On September 6, 1704, the first Apalachee baptism took place in the newly created parish at Mobile.

In September 1763, approximately 80 Apalachees relocated to Rapides Parish, Louisiana. The French established the parish of St. Louis des Appalages so they could continue their religious practices. Knowledge of this Apalachee community was lost until 1996 when ethnohistorians and archaeologists in Louisiana traced them through parish records and contacted the research staff at Mission San Luis. Today, the Apalachee Indians of Louisiana are the only documented survivors of Florida’s once numerous native peoples, and San Luis is the only site in Florida with living descendants of its contact-era indigenous population. The Apalachees of Louisiana have applied for federal recognition drawing, in part, on the research generated at San Luis.