Juan José Flores Aramburu was born on July 19, 1800 in the city of Puerto Cabello, Venezuela, the illegitimate and only son of Juan José Aramburu, a rich and distinguished Spanish merchant from Spain, and to a Venezuelan, Rita Flores Bohorques. Eventually his father returned to Europe, abandoning his only son Juan José Flores and his mother to a life of extreme poverty. Because up to age 14 Juan José Flores received scant formal education, his impoverished mother placed him to learn and work in a Spanish military school and hospital. Since the poor yet sagacious Juan José Flores did not know what to do with his life at age 15 he enlisted as a private in the Spanish Royalist army of Spanish General Pablo Morillo, whose job it was to fight and destroy the patriot armies that were fighting for Spanish American independence in South America. During a short period of time Juan José Flores distinguished himself in Spain's Military for his loyalty, discipline, courage, heroism, and sagacity. However, as a sergeant, he was taken prisoner on October 31, 1817, and at this point he was convinced that freeing his homeland from Spain's domination was a just cause and joined the patriot army of Simón Bolívar. In the Patriot army he became loyal and acquainted with Simon Bolivar, who at an early stage recognized Juan José Flores' outstanding heroism and military talents especially at the victory at the Battle of Carabobo (1821), that at age 23 he was promoted to Colonel and then to Commandant General of the recently freed anti-patriotic royalist city of Pasto.

Juan José Flores' contemporaries described his physical appearance as proud man in military uniform, slender and short but well proportioned, with a handsome countenance that radiates quick intelligence and a commanding presence. Juan José Flores appeared to be self-taught, and despite his scant rudimentary education he became an eloquent orator and an avid reader of contemporary authors such as Rousseau, Montesquieu, Holbach, and Vattel. Juan José Flores was so fascinated with reading that in 1826 he asked for and received a shipment of books from General Santander, then vice-president of the Gran Colombia. Later in life the professors of the University of Quito, recognized Juan Jose Flores' efforts and bestowed an honorary doctorate on Flores in 1842.

On May 13, 1830, the day of Ecuador's breaking away from Gran Colombia, Flores was named supreme chief of the new country, and then on August 14, 1830, he was named provisional President. His official term, however, did not start until September 22, 1830, 11 days after he was elected constitutional President by the assembly in Riobamba. That term lasted until September 10, 1834, and was marked with much turmoil. Flores faced a rebellion led by Luis Urdaneta, a loyalist of Simón Bolívar, who wanted to prevent Ecuador from leaving Gran Colombia. Flores also faced a threat from a member of the Ecuadorian congress, Vicente Rocafuerte, who attempted to overthrow him. Eventually, the two made an agreement – Rocafuerte would become President after Flores, and Flores would become leader of the military. Also during his term, he fought an invading Colombian army in 1832 and again starting in 1834, finally defeating them on January 18, 1835 in Miñarica, near Ambato.

Flores' second term began on February 1, 1839, and ended January 15, 1843. The beginning of his term was marked by peace and social development—he kept his word to rule justly and to defend freedom. However, in the last year of his term, he intervened militarily in the politics of Nueva Granada at the request of the Colombian government, fighting his old enemy, José María Obando. When later forced to intervene again, he was attacked by the Colombian army and his popularity at home fell. Then, after irregularities in the elections of 1842, he pushed to have the 1835 constitution annulled, and the new constitution, nicknamed the "Carta de la esclavitud" ("charter of slavery") allowed him to continue in power for a third term, which began April 1, 1843. During this term, Flores fought to remain in power, but was ultimately overthrown on March 6, 1845 by a rebellion led by Rocafuerte and Vicente Ramón Roca, the man who became the next President of Ecuador.

Flores died of uremia in 1864 while in campaign supporting the presidency of Gabriel García Moreno.