In the forests around Fontainebleau the woodcutters bemoan the winter and the interminable war with Spain. But peace between the two countries is meant to be sealed by the marriage of Elisabeth, daughter of Henri II, King of France, and the Spanish Prince Don Carlos. The latter has travelled to France without revealing his identity to observe his future wife. When they meet in the forest, they immediately fall in love. However, in the meantime, the father of Don Carlos, Philip II, has decided that he will marry Elisabeth himself. While the people celebrate the end of the war, the Princess has to resign herself and Don Carlos is left crushed by his father’s decision.
As he meditates at the monastery of Saint-Just where his grandfather Emperor Charles V is interred, Carlos believes he hears his grandfather’s voice speaking through a monk. Rodrigue, Marquis of Posa and a childhood friend of Carlos returns from Flanders and persuades Elisabeth to meet with Carlos again. He hopes that she will be able to persuade the King to bring peace to the Spanish-occupied Low Countries. The encounter rekindles their passionate love, however, Elisabeth is obliged to remind the Prince that she is now technically his mother. Carlos takes his leave prior to the King’s arrival. The act closes with King Philip confiding in Rodrigue: the former has his doubts about the relationship between his son and the Queen and warns him against the Inquisition.
Celebrations are organised on the eve of Philip’s coronation. The Queen exchanges clothes with Princess Eboli in order to slip out and meet Carlos in the gardens. Believing that he is before the Queen, Carlos effuses words of passion to Eboli. Realising his mistake, and mad with jealousy, Eboli threatens to expose him and the Queen. Rodrigue, who has witnessed the scene, intervenes and intimidates Eboli into silence. He also urges Carlos to leave any compromising documents in his care. As the King is acclaimed by the people, the monks and the Inquisition call for the eternal damnation of the faithless as they prepare for an auto-da-fé. When Carlos Defends the Flemish cause in front of his father, the latter accuses his son of infidelity. Carlos draws his sword but is disarmed by Rodrigue. His intervention is rewarded by the King who elevates Rodrigue to the rank of Duke. The execution of a heretic completes the ceremony.
Riven by jealousy, the King is left in despair at Elisabeth’s rejection and by the attitude of his son. The Grand Inquisitor is not opposed to seeing Carlos condemned to death and he also demands that Rodrigue be handed over to him too. But the king refuses to relinquish his new friend. Meanwhile, the Queen, who has been searching for her missing jewel box discovers that it is in Philip’s possession and that inside it he has found the portrait that Carlos gave to her in the forest at Fontainebleau. Faced with the accusation of adultery, the Queen faints. Eboli, who is in love with Carlos, admits to the Queen that she stole the jewel box to incriminate her. The Queen repudiates Eboli, who also happens to be a former mistress of the King, and she leaves her to choose between exile or a convent. Rodrigue visits Carlos in jail and tells him that he has added some of his own documents to the ones Carlos gave him so that he may be seen to be guilty in Carlos’ place. After he is shot and fatally wounded, Rodrigue has just enough time to pass on the message to Elisabeth that Carlos will be waiting for her the following morning at the monastery in Saint-Just. The King, devastated by the death of Rodrigue, goes to the prison to release his son. However, Carlos rejects him and the people, incited by Eboli, storm the jail to free the prince but the Grand Inquisitor confronts them and restores order.
A distressed Elisabeth prays before the tomb of Charles V and asks to find peace in death. Carlos comes to bid her farewell prior to his departure for Flanders. But just then, the king and the Grand Inquisitor arrive. They accuse Carlos of treason and order his arrest. A monk hides the prince in a cloister. The king and the Grand Inquisitor are left dumbstruck when they in turn believe that they hear the voice of Emperor Charles V.