Born at León, Spain, he was the second son of the 2nd Marquess of Prado and Acapulco and 5th Count of Óbedos, and had a career in the Army, where he became mariscal de campo.
In mid-1760, Juan de Prado was named Governor and Captain General of the Island of Cuba by King Charles III of Spain but did not take possession of his office until February, 1761.
On February 7, 1761, the first works to fortify the heights of La Cabaña, overlooking the bay, and the main fortress el Morro, were begun.
That same year, the city was hit by an epidemic of yellow fever that caused numerous victims among the urban population.
On June 6, 1762, a powerful British expeditionary force under George Keppel began the siege of Havana.