Morales was promoted to captain in 1790. The following year he was promoted to colonel by King Charles IV of Spain, and made commandant of the Third Battalion Cuban Regiment garrisoned at the Castillo de San Marcos in St. Augustine, Florida, which was then a unit of the Captaincy General of Cuba. He arrived there with his daughter Rita Josefa and his grandson Félix Varela, aged two, whose mother, Maria Josefa Ignacia had died a few days after giving birth. In March 1796, Morales, accompanied by royal auditor Gonzalo Zamorano, was appointed to the post of acting governor of East Florida while Governor Enrique White was recovering from an illness, and left it in June of that year, when White recovered and returned to office. During Morales's time as governor, Spanish East Florida was concerned with Georgia's Camden County's failure to curb advancement of "Georgia bandits" on the Florida frontier.
Personal life
On May 17, 1766, Bartolomé married María Medina Barsaga Soledad, the daughter of one of his subordinates, SergeantPedro Medina Barrios, whom he met in 1764 when he was sent to Cuba. Barrios was a small landowner engaged in the production of snuff in the town of Santiago del Prado, where the El Cobre cathedral was located. Bartolomé took up residence there and adopted local folk customs, one of which was devotion to the Virgen Morena, Our Lady of Charity, namesake of the cathedral and linked to Cuban religious tradition. The couple had three daughters in Santiago: Maria Josefa Ignacia, Rita Josefa, and Maria Josefa Morales. The eldest daughter died a few days after giving birth to her son Félix. Consequently, Félix was raised mostly by his aunt Rita. After serving as commander in Florida, Bartolomé settled there in 1790 with his daughter Rita and infant grandson, Félix Varela. Bartolomé wanted his grandson to go into the military, and when the boy reached age 14, proposed that he enroll as a cadet in a military academy. Félix refused, saying that his vocation was not to kill people, but to save them, and asked permission to enter a seminary to become a priest. Father Félix later became an important figure in the history of Latin America. The FatherFelix Varela Center in Jacksonville, Florida, belonging to the Diocese of St. Augustine, Florida, is named for Bartolomé's grandson, Félix Varela.
