[9][b] In September of 1464, Pacheco assembled his allies at Burgos and published a manifesto condemning Henry IV's mismanagement and the excessive privileges granted to Beltrán de la Cueva.

[16] In February 1465, he renounced Alfonso as his heir, commanded Beltrán to mobilize a royal army, and ordered Infanta Joanna, Queen Joan, and his younger half-sister Isabella to be moved to Segovia under heavy guard.

[17] Civil war broke out in June 1465 after Carrillo, Pacheco, and other agitators conducted a ceremonial deposition-in-effigy of Henry outside the city of Avila and crowned Alfonso as a rival king.

[14][18] Around this time, Henry's opponents began to contest Joanna's legitimacy on the grounds that her parents never received the necessary papal dispensation for marriage within four degrees of consanguinity.

[20] After rebels captured Segovia in 1467, a six-month truce was agreed to that arranged for the royal treasury and jewels to be returned to Henry's safekeeping in exchange for Joanna's mother, Queen Joan, to live at Archbishop Fonseca's castle as a guarantee.

[30] Íñigo López de Mendoza, 1st Count of Tendilla, who had been appointed guardian of Joanna by Henry in 1465, distributed a letter to Castile's most powerful barons condemning the settlement and issued a formal protest to Pope Paul II.

In another, he had reconciled the Mendozas to the king and provided Princess Juana with a chance to compete dynastically for the crown.However, Isabella refused to consent to the arrangement and instead married Ferdinand of Aragon in 1469.

On 26 October 1470, she was betrothed and then married by proxy to Charles, Duke of Guienne, brother of Louis XI of France, and proclaimed as the legitimate heir to the throne.

After a few unsettled arrangements, which included French and Burgundian princes, Joanna was promised in marriage to her maternal uncle, King Afonso V of Portugal, who swore to defend her (and his own) rights to the Crown of Castile.

In addition to the King of Portugal, Joanna was supported by some of the high Castilian nobility and by descendants of Portuguese families that had settled in Castile after 1396: the Archbishop of Toledo (Alfonso Carrillo de Acuña); the 2nd Duke of Escalona, a powerful and wealthy nobleman; the Estúñiga family, with lands bordering Portugal; the Marquess of Cádiz; and the Grand Master of the Order of Calatrava, Rodrigo Téllez Girón.

His son Prince John of Portugal defeated the Castilian right wing, recovered the lost Portuguese Royal standard, and held the field, but overall the battle was indecisive.

[38] Even so, the prestige of Joanna and Afonso V dissolved because Ferdinand II sent messages to all the cities of Castile and to several other kingdoms informing them about a huge victory where the Portuguese were crushed.

[44] In 1482, Afonso's successor, John II, began considering wedding Joanna to King Francis Phoebus of Navarre, nephew of Louis XI of France.

In March of the same year, John was asked to swear an oath to Isabella's ambassadors that he would not permit Joanna to marry, leave Portugal, or forgo monastic life.

[48] In 1522, Joanna relinquished her title as queen of Castile and offered the crown to John III of Portugal, citing her age and inability to produce an heir as reasons for her abdication.