He was the second surviving son of Albert V, Duke of Bavaria, and his wife Archduchess Anna of Austria, and consequently was prepared for a military career.

Ferdinand's older brother earned for himself the sobriquet "the Pius" for his melancholy demeanor, his ardent attachment to prayer and meditation, and, more obviously, for his eschewal of hunting, dancing, and other frivolities that dominated social life in a 16th-century court.

As he and the archdukes Ferdinand and Maximilian heard the mass, the population harassed the celebrant priests, and interfered with the conduct of the procession itself.

[4] His younger brother, Ernst, was elected to the Archbishopric of Cologne, in 1583, as part of the conflict over the control of the electoral see.

Ferdinand took command of his brother's army during the Cologne War; his able management of the army, plus the support of troops from the Duke of Alba in the Spanish Netherlands, secured the electoral dignity for his brother, and consolidated the family's place in imperial politics.