Between 1539 and 1543, he lived with family members in Barcelona coinciding with his father's stint as Viceroy of Catalonia.
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There he worked as an intermediary between the court of Sebastian of Portugal with Margaret of Valois.
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Fernando was the son of Juan de Borja y Castro, I Count of Mayalde and his wife, Francisca de Aragón y Barreto, Countess of Ficalho, and paternal niece of Francisco de Borja who was also Fernando's paternal grandfather.