Act 1
In the forest of Fontainebleau.
The Spanish prince Don Carlo has travelled incognito to France to discreetly observe the king of France’s daughter whom he is supposed to marry in order to bring an end to the war that has pitted the two enemy powers against each other. When Don Carlo stumbles across Elisabeth in the forest, they both fall instantly in love.

However, both are unaware that Don Carlo’s father Philip II has decided to marry the young Elisabeth himself. As the people celebrate the end of the war, Elisabeth is forced to accept her unexpected fate. Don Carlo cannot conceal his distress.

Act 2
Carlo goes to the monastery of Saint-Just to meditate at the tomb of Emperor Charles V. Whilst there, Carlo thinks he hears the voice of the deceased Emperor, his grandfather, in the voice of a monk. Still haunted by his lost love, Carlo reveals his despair to his childhood friend Rodrigue, the Marquis of Posa, who has just returned from the Low Countries which are currently enduring the harshness of Spanish occupation. Rodrigue urges Carlo to withdraw from the court and leave with him to defend the Flemish cause.

As the king and queen meditate at the tomb of Charles V, Elisabeth’s ladies-in-waiting and Princess of Eboli enjoy themselves at the gates of the monastery. Rodrigue convinces Elisabeth to meet with Carlo again in the hope she will be able to persuade the king that Carlo has the means to bring peace to Flanders. Although the encounter reignites the smouldering passion of their former love, Elisabeth reminds Carlo that she is now his mother.

Not long after Carlo leaves, the king arrives. However, the latter is surprised to find the queen alone, which is counter to royal etiquette. Philip banishes the queen’s lady companion from the court and dismisses the courtiers accompanying her. Posa, alone with the king, uses the occasion to plead for the Flemish cause. The king, charmed by Rodrigue’s freedom and independence, opens up and cautiously expresses his doubts as to the true nature of the relationship between his son and the queen. He also advises him to be wary of the Inquisition.

Act 3
A ball is to be held on the eve of Philip’s coronation.
The queen prefers not to attend and suggests that Princess of Eboli exchange clothes with her to allow her to discreetly slip away. The princess, secretly in love with Carlo, arranges to meet him in the queen’s gardens. Believing he is meeting Elisabeth, Carlo showers her with passionate locutions that Eboli thinks are intended for her. Disabused, she finally realises that Carlo loves the queen and, mad with jealousy, she threatens to denounce them. Rodrigue, who has witnessed the scene, intervenes and threatens Eboli in no uncertain terms.

Understanding the seriousness of the danger, Rodrigue advises Carlo to entrust him with any compromising documents he might have in his possession. The people acclaim their king, the monks and the Inquisition and call for the damnation of the infidels during the preparations for the auto-da-fé. Leading a delegation of deputies from Brabant and Flanders, Carlo defies protocol and, without informing Rodrigue, throws himself at Philip’s feet in the hope that the latter will listen to his pleas. The king flies into a fury and reproaches them for their disloyalty.

Carlo draws his sword against his father. No one dares to intervene except for Rodrigue who, eager to avoid the worst, stops Carlo and disarms him. Carlo for his part is stunned by what he perceives as his friend’s betrayal. Philip announces that Rodrigue is to be elevated to the rank of duke. The ceremony ends with the death of a heretic.  

Act 4
Having retreated into sombre solitude, the jealous king despairs at Elisabeth’s rejection and the attitude of his son. Torn as to whether he can condemn his own son to death, he seeks the opinion of the Grand Inquisitor. God sacrificed his own, replies the latter who also asks Philip to deliver Rodrigue to him, whom he accuses of having dangerous and subversive ideas. During a harsh exchange of words, the king refuses to hand over his new, unexpected friend. The queen demands justice from her husband for the theft of her jewel box but she is astounded to find it in Philip’s possession. The latter opens the box in front of her to reveal the picture of Carlo that the latter gave her in the forest at Fontainebleau. When Philip angrily accuses her of adultery, the queen faints.

Remaining alone with the queen, Princess of Eboli is overcome with remorse and admits to having stolen the jewellery box in order to falsely implicate the queen. Not only does she express her true feelings for Carlo but she also reveals that she was the king’s mistress. Elisabeth offers her the choice between exile and a convent. Rodrigue visits Carlo in prison and tells him that he will soon be freed. He also lets him know that the compromising documents which Carlo gave him for safe keeping have been found at his home.

To these, he has added others that will prove to the king that Rodrigue and Rodrigue alone is guilty. A shot rings out. Fatally wounded, Rodrigue falls to the ground. He has just enough time to tell the Prince that Elisabeth will be waiting for him the next day at the Monastery of Saint-Just. On seeing Rodrigue’s body, the king, who has just freed his son and admitted his error, is overcome with grief and mourns for the man who managed to bring him out of his solitude. He seeks to be reconciled with his son but Carlo scorns his overtures. Incited into a fury by Eboli, the people storm the prison to free Carlo. However, the Grand Inquisitor’s intervention sows terror and the people ultimately bow before God and the king.

Act 5
Devastated by grief, Elisabeth prays before the tomb of Charles V and asks for peace in death. Carlo comes to bid farewell before leaving for Flanders. Their last emotional meeting is interrupted by the arrival of the king and the Grand Inquisitor.

The latter accuses Carlo of treason and orders his arrest but a monk leads the prince into the deepest recesses of the cloister. The king and the Grand Inquisitor are left dumbstruck after they too believe they have heard the voice of Charles V.