Book 1. The legend of the Knight of the Red Crosse, or of Holinesse

Canto i Redcrosse and Una are travelling, when a storm drives them into a wood where Redcrosse kills the dragon Error. Archimage welcomes them in his hermitage, but produces sexual illusions that destroy their mutual trust, and Una goes on alone.
Canto ii Archimage disguises himself as Redcrosse and follows Una, while Redcrosse accompanies Duessa whom he takes for Una, after killing Sansfoy.
Canto iii Una, alone, is befriended by a lion and finds refuge with Ignorance and Blind Devotion. Archimage finds Una, but is defeated by Sansloy who carries her off.
Canto iv Redcrosse with Duessa comes to the House of Pride and sees the procession of the Deadly Sins. Sansjoy challenges Redcrosse, and receives favours from Duessa.
Canto v After the battle, Duessa and Night carry the wounded Sansjoy to the Underworld for healing. Redcrosse escapes from the House of Pride, still with Duessa.
Canto vi Satyrs rescue Una from Sansloy, and she is assisted by Satirane.
Canto vii The giant Orgoglio overpowers Redcrosse, puts him in prison, and takes Duessa as his mistress. Her servant dwarf tells Una what has been happening to Redcrosse; she meets young prince Arthur who promises to save Redcrosse.
Canto viii Arthur kills Orgoglio, wounds his tame beast, punishes Duessa, and rescues the weakened Redcrosse.
Canto ix Arthur tells Redcrosse the story of his strange meeting with the Faerie Queene Gloriana. Redcrosse and Una see the Cave of Despair and Redcrosse is tempted to suicide.
Canto x Redcrosse is brought by Una to the House of Holiness where he recovers his strength. He is shown the heavenly Jerusalem.
Canto xi After a 3-day battle Redcrosse kills the dragon and sets free the royal parents of Una.
Canto xii Redcrosse is engaged to Una, but the time is not yet ripe for their marriage.

Book II. Sir Guyon, or of Temperance

Canto i Archimage urges Guyon to attack Redcrosse; they become friends instead, before Redcrosse rides away. Guyon and the Palmer accompanying him find Amavia with her baby, its hands bloodstained.
Canto ii The fountain cannot cleanse its hands.
Canto iii The baby is left at the castle of Medina. Braggadochio steals Guyon's horse, meets Trompart with Archimage. Belphoebe encounters Braggadochio with Trompart.
Canto iv Guyon overpowers Furor, stops Occasion, and rescues Phedon who tells his story. Pyrochles approaches.
Canto v Pyrochles fights Guyon and frees Furor before going to Acrasia's bower in search of Cymochles.
Canto vi Cymochles is persuaded to visit Phaedria's island, Phaedria takes Guyon there, without the Palmer; the two knights fight until Phaedria parts them.
Canto vii Guyon visits the Cave of Mammon, where he sees the throne of Philotime (Mammon's daughter) and the Garden of Proserpine. He emerges exhausted.
Canto viii Arthur saves Guyon from Pyrochles and Cymochles.
Canto ix Guyon tells Arthur about the Faerie Queene; they drive off the besiegers of the Castle of Alma and explore it.
Canto x Arthur reads the history of the kings of Britain, up to his own still unknown father; Guyon reads of the kings of Faerie (descended from Prometheus's creation Elf).
Canto xi Arthur fights with Maleger
Canto xii Guyon visits and destroys Acrasia's Bower of Bliss.

Book III. Britomartis, or of Chastity

In Canto i Guyon and Arthur meet Britomart, disguised as a knight; as they pursue Florimell they are separated. Britomart arrives at the Castle Joyeous and meets Redcrosse. Britomart tells of her quest for Arthegall; in retrospect we learn how she fell in love with Arthegall after seeing him in a magic mirror, left home, and consulted Merlin in his cave. He told her the identity of her lover, as well as describing the future destiny of their descendants, the British kings. After this, she set out disguised as a knight. Encountering Marinell, she wounds him. Meanwhile, Arthur has gone on following Florimell, whose story he hears. His squire Timias has been pursuing a forester, who wounds him. He is helped by Belphoebe, with whom he falls in love. In Canto vi The birth of Belphoebe, and her twin sister Amoret, is told. Begotten by the power of the sun, they emerge from their mother's womb as she sleeps; Diana and Venus each take one child, Venus takes Amoret to grow up in the Gardens of Adonis, which are described. Florimell nearly falls into the power of a witch and her son. Satyrane enters the quest for Florimell. But a false Florimell is made by the witch for her son; this is stolen and causes confusion. Britomart forces a way into Malbecco's castle, where Paridell seduces Malbecco's wife. In Canto xi Britomart and Satyrane are separated. Britomart meets Scudamor and undertakes to rescue Amoret who is in prison in the House of Busyrane, where she sees the Masque of Cupid, and frees Amoret.

Book IV. Cambel and Telamond, or of Friendship

Amoret at last discovers that Britomart is a woman; Duessa and Ate riding with Blandamour and Paridell encounter them, then a fight begins when they meet up with Scudamour and Glauce. Finally they meet Cambell and Triamond with their wives Canacee and Cambine (from Chaucer's The Squire's Tale); their story is told. The false Florimell chooses Braggadochio after a tournament for Florimell's girdle. In Canto v Satyrane visits the House of Care. In Canto vi Britomart fights with Arthegall, who then begins to woo her before setting out on his quest, while Britomart and Scudamour go looking for Amoret. Belphoebe and Timias rescue Amoret from Lust, Arthur finds Amoret with Aemilia, they set out together. In Canto x Scudamour tells how he wooed Amoret in the Temple of Love. Canto xi celebrates the marriage of the Thames and the Medway. Marinell falls in love with Florimell, she is released.

Book V. Artegall, or of Justice

Artegall, brought up by Astraea, sets out on his quest, and after various adventures overthrows the giant Democracy. In Canto v he is imprisoned by Radigund. Britomart is told of this, and in Canto vii visits Isis Church before killing Radigund and rescuing Artegall. Arthur and Artegall rescue a prisoner, catch Guile, and see the trial of Duessa. The rest of the book tells of Artegall's adventures until at last he meets Envy, Detraction, and the Blatant Beast.

Book VI. Calidore, or of Courtesy

The adventures of this book, centered on Calidore, show various victims being rescued from the uncourteous, who are punished. Arthur and Timias are reunited, then parted again. In Canto ix Calidore first comes upon Pastorella, whom he woos. He sees the Graces dance, and rescues Pastorella from a lion; she is captured by brigands, and wooed by their captain who saves her when the others want to sell her. Calidore disguises himself and rescues Pastorella, whose long-lost parents are discovered. Finally, Calidore conquers the Blatant Beast.