The city was named for the Count of Linhares, who inherited the land of the 3rd General Governor of Brazil, Mem de Sá (c. 1500 – 2 March 1572).

[4][5][2] Gaspar Pinto dos Reis and his wife donated land near the town center to the Franciscans 1629.

[4][2] São Francisco do Conde retains numerous cultural traditions due to its history of slavery and large Afro-Brazilian population.

The town is noted as a center of the Candomblé religion, capoeira, and capa bode, masks created by Bantu slaves from Angola, now worn during Carnival.

[6] São Francisco do Conde is home to numerous historic structures, many designated as Brazilian national and Bahian state monuments.