The forest of Fontainebleau in France
Don Carlos, son of King Philip of Spain and heir to the throne, is to be married to Elisabeth of Valois, daughter of the King of France. Secretly and against his father's orders, he has joined the party of the ambassador, the Count of Lerma, and gone to France to see his bride.
He has seen her and fallen in love with her and when she loses her way after a hunting party he meets her, gives her his portrait, makes himself known and confesses his love, which is returned.
But their dream of happiness is cut short by the news, brought by the page Thibaut, that it has been decided that Elisabeth should marry Philip. Alhtough she is given an apparently free choice, it is clear that the peace between the two countries depends on her acceptance and she submits.
Scene 1: The tomb of the Emperor Charles V at the monastery of San Yuste
Carlos laments the loss of Elisabeth as monks chant the obsequies of the emperor. He thinks he recognises in one of the monks the dead emperor in person.
He is joined by his friend Rodrigo, Marquis of Posa, who exhorts him to help the Flemish people who are suffering under the heavy Spanish yoke. Carlos confides that he loves his stepmother, and the two swear eternal friendship and dedication to the cause of liberty, while Philip and Elisabeth kneel at the tomb.
Scene 2: A garden at the gate of the monastery
The queen's ladies are gathered. The Princess of Eboli, accompanied by the page Thibaut, sings a song. When the queen appears the Marquis of Posa is announced. Along with letters from France he gives her a letter from Carlos. As she reads it he is engaged in polite conversation with Eboli. Posa then begs the queen to intercede with the king for Carlos, who is suffering from his displeasure.
Carlos appears and all withdraw to allow him to be alone with the queen. He begins quietly, asking for her help with the king, but becomes more emotional, lamenting his lost love and collapses at her feet. She is distressed and he recovers and wildly declares that he loves her. She answers indignantly, as becomes the wife of his father, and he rushes from her presence in self-loathing and despair. The king arrives and, angry at finding the queen alone, dismisses the lady who should have been with her and orders her to return to France. Elisabeth takes an affectionate farewell of her and leaves.
The king detains Posa, who is about to go, and asks why he has never sought favor from the king, though he has deserved it. Posa answers that he wants nothing for himself, but begs for peace for the people of Flanders. The king offers peace brought about by the sword, pointing to Spain as an example, but Posa cries out that this is the peace of the grave. Philip pardons his freedom fo speech but warns him against the grand inquisitor. He confides his fears that his wife and son are betraying him and authorises Posa to visit the queen at any time to investigate this suspicion.
Scene 1: The queen's garden
Carlos has received a letter giving him an assignation, which he thinks is from the queen; but he finds instead the Princess of Eboli, who is in love with him. Mistaking her at first for the queen, he greets her ecstatically, only to draw back in horror when he realises his mistake. She quickly leaps to the conclusion that it is the queen he loves and threatens exposure.
Posa appears, and after trying unsuccessfully to convince her that Carlos is raving, tries to kill her to stop her from speaking. But he is prevented by Carlos, and she leaves, still threatening vengeance. Posa asks the prince to give him any secret documents he has.
Scene 2: A square in Madrid
An auto-da-fe is in progress and the crowd acclaims the glory of the king, who emerges from church and repeats his vow to have the wicked put to death by fire and the sword. Carlos leads in a group of Flemish deputies who beg for mercy for their country, but the king angrily rejects them as traitors.
Carlos then asks the king to allow him to go to Flanders as his deputy, but the king refuses, claiming that he would then be able to seize the throne. Carlos draws his sword to swear faith with the Flemish people and Philip orders him to be disarmed. Only Posa obeys and demands the sword, which is yielded by the stunned prince. The auto-da-fe continues, but a voice from heaven promises peace to the victims.
Scene 1: The king's study
The king broods that his wife has never loved him. In answer to his summons the grand inquisitor appears and Philip confides his suspicion that the prince is planning rebellion. They agree that he should be handed over to the Inquisition, but then the inquisitor demands that Posa be handed over as a far greater heretic. The king refuses, is denounced by the inquisitor, and then tries to make his peace with him, though resentful that the throne has to always give way to the church.
The queen rushes in demanding justice, as her jewel casket has been stolen. It has in fact been given to Philip, who orders her to open it. The portrait of Don Carlos is revealed and she defends this on the grounds that he had once been promised as her husband. When the king abuses her and accuses her of adultery, she faints and he calls for help. Eboli and Posa appear, the latter reproaching the king for his lack of self-control.
When the two women are left alone, Eboli confesses that it was she who betrayed the queen, jealous because she too loved Carlos, but in vain. The queen pardons her, but when Eboli confesses that she has been the king's mistress, Elisabeth orders her either to a convent or to exile, leaving Eboli to curse the fatal gift of beauty which led to her downfall.
Scene 2: An underground prison
Posa visits Carlos in prison and tells him that the papers he took from Carlos have been found in his possession and have proved him to be the leader of the rebellion. Posa is shot by an officer of the Inquisition and dies happy that he has been able to preserve Carlos to save Flanders. He tells him that Elisabeth will explain everything to him the next day at the emperor's tomb.
Philip, accompanied by grandees, appears and offers Carlos back his sword, but he accuses his father of the murder of Posa, whose death the king also mourns. The people are threatening revolt unless the prince is set free. The king orders the gates to be opened and they surge in, but are subdued when the grand inquisitor orders them to kneel before their king.
The tomb of Charles V at San Yuste
Elisabeth kneels in prayer at the tomb. She remembers happier days in France, and prepares to see Carlos for the last time. When he arrives he declares that honor has vanquished love and that he is ready to go to Flanders. They promise to meet in a better world, but their farewell is interrupted by the king, with the grand inquisitor and officers of the Inquisition.
Carlos draws his sword to defend himself but is suddenly drawn into the monastery by the mysterious monk, his disguise thrown off, now revealed as the emperor.