In 1509 the queen Juana I of Castile arrives at Tordesillas with the corpse of her husband, which is deposited in Santa Clara for thirteen years until it is moved to Granada. She will be shut in here for 46 years until her death in 1555 when she was 75 years old.
In 1517, Carlos I, who come with her sister Leonor, visits his mother in the Palace of Tordesillas for the first time, they will continue throughout the years. At the same time, the Court was established in Tordesillas temporarily. This year solemn honorary funerals are celebrated by Philip "the Handsome".
Tordesillas was a scene for some events in the war of the Communities. On August 29, 1520, Padilla had an interview with Doña Juana to request the support of the unique and legitimate sovereign. The Holy Meeting moved there from Avila, on September 19, 1520. Doña Juana listened to their claims, supported them, but she did not sign the decrees they were asking her to sign whose aim was to destroy D. Carlos, her son, as king. On December 5, 1520 the troops of the count of Haro take Tordesillas and on April 23, 1521 the commoners suffer a definitive defeat in Villalar. The casualties of the above-mentioned battle were moved to Mater Dei Hospital.
In 1525, the Infanta Catalina leaves Tordesillas to marry the Portuguese king Juan III, therefore, the one who was queen and regent of Portugal lived in Tordesillas together with her mother Juana I of Castile for almost 16 years. The same year, Philip "The Handsome " remains are moved to Granada.
On Holy Friday, on April 12, 1555 the death of Queen doña Juana I of Castile takes place at the age of 75, after living in Tordesillas for 46 years.
In 1574, Doña Juana's corpse, buried in a simple grave in the presbytery of the Conventual Church of Santa Clara, is moved to "El Escorial" in order to move her to the Royal Chapel of Granada later, where, nowadays, her remains rest together with her parents' and husband's.
In 1592, Philip II visited Tordesillas, where he had been several times already when he was the prince and where he had a few private rooms in the Royal Palace.
In 1603 the Franciscan order arrives at Tordesillas by desire of Philip III.
In 1636, the medieval bridge was rather affected by the great overflow on river Duero that took place in this epoch.