Barabas stands out because of his differences. The fact that he is rich, Jewish, and secretive alienates him from Christian Maltese society. Initially, Barabas's only motivation is money. Gradually, however, he grows to loathe his Christian enemies and notions of vengeance begin to consume him. The protagonist goes on a killing spree and murders an entire convent of nuns, along with his daughter, his slave, two young men, two priests, a pimp, and a prostitute. It becomes apparent that Barabas kills because of desire and not because of need. Although the narrator suggests in the Prologue that Barabas is a Machiavellian—Machevill states that his "money was not got without my means"mdash;in reality Barabas has little in common with the real political author. He does, however, personify all the traits that an Elizabethan audience would have understood as quintessentially Machiavellian. He is strategic, dishonest, power-hungry (at least in the sense that he desires to have power over his enemies) and irreligious. But as a dramatic amalgamation of all these different evils, Barabas is a slippery protagonist. A profound ambiguity lies at the heart of his character. His introduction as a comic glutton who "smiles to see how full his bags are crammed" has little in common with his later characterization as a vengeance-obsessed psychopath. Barabas is simultaneously a scheming manipulator who feels no pity for his hapless victims and a greedy old man who jealously guards his wealth.

Marlowe's ambiguous characterization is complicated by the fact that Barabas often earns our commiseration, if not our sympathy. In a society of religious hypocrites, the protagonist is refreshingly honest about his own motives. Although he is accused of being a traitor in Act V, scene ii, earlier scenes show that he was never accepted as a citizen of Malta from the start. He is avaricious, jealous, resentful, and controlling, but he also professes great love for his daughter Abigail. The protagonist is deeply embittered by her conversion and by Ithamore's treachery, which leaves him without an heir. Marlowe intends for our reaction to his character to be profoundly uncertain. At the play's end, Barabas declares his own fantastical notions of destroying the world and dies uttering, "I would have brought confusion on you all, / Damned Christians, dogs, and Turkish infidels." Marlowe's treatment of his character is thus deeply ironic, for we never know whether the playwright is taking stereotypes of Jews or Machiavellians seriously. Marlowe's readers must decide whether he is pandering to these stereotypes or undermining them through satire.