Ferneze enters, instructing his soldiers to fortify the town in the face of an impending Turkish assault. Bellamira and Pilia-Borza appear and reveal Barabas's crimes to the governor. Ferneze orders that the protagonist be brought to him, along with Ithamore, who will provide proof of Barabas's crimes. When the two men arrive, Barabas tries to deny the charges, but Ithamore admits to everything. The merchant pleads with Ferneze to "let me have law," to which the governor replies, "you shall have law." Barabas leaves, mumbling that he hopes the poisoned flowers will work soon.
Katherine arrives, and Ferneze tells her the truth about Mathias's death. She is vitriolic about Barabas, but the governor assures her that he is in jail waiting to receive justice. An officer tells Ferneze that both of the prisoners, along with the pimp and the prostitute, are dead. The governor orders that Barabas's body be thrown over the city walls to "be a prey for vultures and wild beasts." Once this has happened, Barabas gets up and explains that he feigned death by taking a sleeping draught. He vows to help Calymath and be revenged on the Christians in Malta. Barabas finds Calymath and explains that he knows a secret passage whereby 500 troops can enter the city and open its gates. Calymath promises to make Barabas governor if he is telling the truth. The merchant states "let me die" if Calymath finds he has lied.
A victorious Calymath enters with his Maltese captives. He assures Ferneze that the prisoners will "under Turkish yokes groaning bear the burden of our ire," before he tells Barabas that he has been made governor. Ferneze despairs at this appointment and at Barabas's treachery, crying, "What greater misery could Heaven inflict?" Calymath leaves, promising the new governor that he will be guarded by his "Janizaries." Barabas sends the captives to prison and wonders about his security. He concludes that many people hate him and that his life would be under threat as governor of Malta. Barabas concludes that he will only maintain his position "bravely by firm policy."
Barabas calls back Ferneze. Barabas asks him what he thinks will come of the state, and Ferneze replies that he sees "no reason but of Malta's wrack." The protagonist assures Ferneze that he will help free Malta and her captured soldiers. Amazed, Ferneze assures Barabas that he will give him an enormous sum of money if the Jew will "[d]eal truly with us as thou intimatest." The protagonist explains that he will invite Calymath to a feast at which Ferneze will only have to perform "one strategem" in order to rid Malta of the Turks. The Ferneze offers Barabas his hand and states that he will deliver his money in the evening. Ferneze departs, and Barabas assures himself that he will make "a profit of my policy." Barabas leaves to plan the details of his deadly feast.
Once again, Barabas finds himself brought before the governor. Barabas meets his accusers in Act V, scene i with a measure of proud disdain, asserting, "I'll go alone; dogs, do not hale me thus." Clearly, his cold reserve contrasts with the self-righteous emotion displayed by the other characters. Ferneze, who dramatically orders Barabas away from him with the words "his sight is death to me," appears particularly pompous and moralistic. Society's prejudice is shown by the fact that Barabas is only referred to as "the Jew" in this scene, even though he is not the only Jewish person in Malta. Our reaction to Barabas's unmasking is thus ambiguous. A measure of relief that he is being brought to justice is countered by a sense of disgust at society's hypocrisy.
Marlowe levels a charge of legalism—meaning a pedantic observance of the letter rather than the spirit of the law—against Barabas in Act V, scene i. The protagonist's demand to "have law" echoes Shylock's determination to have his pound of flesh in Shakespeare's The Merchant of Venice. Barabas knows that none of the charges against him "can prejudice my life." Are we to believe Barabas, or has the Barabas deluded himself into thinking he is invincible? The playwright leaves his audience to decide whether Barabas's knowledge of the law is accurate, or if he has lost whatever grasp of reality he has had left. Ferneze's response is typically evasive: the governor seems to promise everything and nothing. Barabas appears almost comically homicidal by the end of this scene; even as he is led to jail he mumbles his hope that the "poisoned flowers will work anon." The audience is left wondering whether the great criminal mastermind has become a murmuring madman.