Act I
The morning after a revolt by the Streltsy militia that saw much bloodshed, Moscow begins to return to normal. Shaklovity, a diplomat, dictates to a clerk a letter in which he claims that the Khovanskys - both father and son - were the instigators of the revolt. The clerk reads aloud the list of those perished during the revolt. Prince Ivan Khovansky, head of the Streltsy, leads his squad to patrol the city of Moscow. Ivan Khovansky’s son, Andrei, pursues a German girl called Emma. Marfa, Andrei’s former lover, tries to protect Emma, but then Ivan Khovansky commands the Streltsy to take the German to his chambers for himself. Andrei does not want to surrender the girl to his father, and the two prepare to fight. Dosifei, leader of the schismatics, stops them just in time. He appeals to them to forget their disagreements and to unite in the face of upcoming misfortune - the division and downfall of Russia.
Act II
Prince Golitsyn, an all-powerful minion of the regent Sophia, has summoned Marfa to tell his fortune. When she foretells his forthcoming disgrace and exile, the frightened Golitsyn gives the order to have Marfa drowned. Prince Ivan Khovansky comes to Golitsyn followed by Dosifei, who in his layman past was known as Prince Myshetsky. Each one of them fails to persuade the others as to the right action to take against the young Tsar Peter. Marfa returns and tells how Peter's soldiers rescued her from her execution. Shaklovity brings a frightening piece of news: Tsar Peter has received the accusation against the Khovanskys and has ordered an investigation.
Act III
Susanna, a schismatic, judges Marfa for giving in to sinful temptation. Dosifei stands by Marfa and condemns Susanna for speaking ill of another. Shaklovity enters the place where the Streltsy are sleeping. He is worried for Russia's future and wonders what sort of force is needed to save her from her enemies. After the Streltsy wake up, a clerk brings them grave news: Peter’s troops are on their way towards them. The Streltsy call for Ivan Khovansky to give them orders. But Khovansky refuses to lead the Streltsy into battle and advises them to disperse to their homes.
Act IV
Ivan Khovansky is ill at ease even though he feels safe inside his own house. Varsonofyev, a minion of Prince Golitsyn’s, tells Khovansky that he is in danger, but Khovansky ignores the warning and has the messenger flogged. He orders his Persian slaves to dance for him but then Shaklovity enters and assassinates him.
The disgraced Prince Golitsyn is sent into exile. Dosifei reflects on the fate of the two princes. Marfa informs him that the Old Believes will be Tsar Peter’s next target. Andrei confronts Marfa about Emma, as the girl has been sent across the border, out of his reach. When Andrei attempts to summon the Streltsy, they appear bearing instruments for their own execution. Marfa offers Andrei asylum amongst the Old Believers instead. The condemned Streltsy pray for God’s mercy but their wives insist that they should be executed as planned. At the last moment, a guard proclaims that Peter has pardoned them.
Act V
Dosifei and his followers have taken refuge in a hermitage. Rather than be captured by the Tsar’s men, he exhorts the brethren to prepare for martyrdom. Andrei is still looking for Emma but Marfa reminds him of their own love and promises not to leave his side. As the Old Believers prepare their funeral pyre, they hear Peter’s soldiers approaching. Marfa lights the pyre and the schismatics sing a final hymn as they commit mass self-immolation.