Antonio Flores was born in Quito at Carondelet Palace (the presidential residence) while his father, General Juan José Flores, presided over the nation.

His mother was Mercedes Jijón de Vivanco y Chiriboga, daughter of the Count of Casa Jijón, member of one of Quito's old aristocratic families.

During the first presidency of Gabriel García Moreno, Flores was an ambassador in Paris, London, and Washington.

He was married to Leonor Ruiz de Apodaca y García-Tienza, a native of Cuba.

His vice president and predecessor was Pedro José Cevallos.