As with Shakespeare's Merchant of Venice, the unremitting evil of The Jew of Malta's anti-hero leaves the play open to accusations of anti-Semitism. However, like Shakespeare's Shylock, Barabas also shows evidence of humanity (albeit rarely), particularly when he protests against the blatant unfairness of the governor's edict that the Turkish tribute will be paid entirely by Malta's Jewish population. It is because of Barabas's protests that he is stripped of all he has and consequently becomes a sort of monster. He has more asides than any other character, making his isolation from the other characters, including his fellow Jews, all the more evident, and he constantly has to operate in what he does alone: even his daughter becomes detached from him before long, and Ithamore, too, soon loses interest in his former loyalty towards his master. In his first meeting with Ithamore he has his most famous speech that begins: "I walk abroad a-nights/ And kill sick people groaning under walls," and follows this with over twenty more lines about various murders and robberies he has apparently performed. Some have interpreted Barabas by suggesting that nothing in his personality implies that so underhanded a character would suddenly come out with the truth as he does, and it is possible that he is not even speaking the truth at all. This has led some to suggest that, in a sense, the Jew of Malta is a play about his transforming into, rather than actually being from the beginning, the very thing that anti-Semites all around him portray him as. Indeed, it could be for this reason that Machievelli, in the Prologue, describes it as the "tragedy" of a Jew.
Barabas says that, in his continual acts of treachery, he is only following the Christian example. He notes that according to Catholic teaching, "Faith is not to be kept with heretics", to which he adds "And all are heretics that are not Jews" (Act II). Barabas also says in the same act:
Good sir, Your father has deserv'd it at my hands, Who, of mere charity and Christian ruth, To bring me to religious purity, And, as it were, in catechising sort, To make me mindful of my mortal sins, Against my will, and whether I would or no, Seiz'd all I had, and thrust me out o' doors, And made my house a place for nuns most chaste.
This reference to the example set by Christians is similar to Shylock's famous "Hath not a Jew eyes?" speech in Act III, Scene 1 of "The Merchant of Venice," which concludes:
If a Jew wrong a Christian, what is his humility? Revenge. If a Christian wrong a Jew, what should his sufferance be by Christian example? Why, revenge. The villany you teach me, I will execute, and it shall go hard but I will better the instruction.
Meanwhile, very few of the play's other characters show significant redeeming qualities. The play ridicules Christian monks and nuns for engaging in forbidden sexual practices, and portrays a pair of friars trying to outbid each other to bring Barabas (and his wealth) into their order. Malta's Christian governor, in addition to his unfair treatment of the city's Jews, is revealed to be a grasping opportunist who seizes any chance to get an advantage. The Turkish slave Ithamore is somewhat idiotic and has no qualms about getting drunk when offered wine (and sex) by a prostitute (quite apart from his role in multiple murders), and aside from him there are the Turkish invaders who plan to make the city's defenders (the Knights of Malta) into galley slaves.
The play portrays characters of three religious groups—Christians, Jews, and Muslim Turks—in constant enmity with one another. It satirises self-contented morality and suggests that, in the end, all religious groups are equally likely to engage in violent and selfish acts, regardless of their professed moral teachings. This irony comes to a head when Barabas, falling into his own boiling cauldron, cries out to the Christian and Turkish onlookers for mercy. Barabas, of course, would have shown the Turks no mercy had they fallen prey to his trap, and yet expects help from his erstwhile Christian victims and intended Turkish ones. Meanwhile, he has been derided throughout the play by Christians for not showing proper Christian charity, and yet the play's Christians show him no mercy when he is in need of help. The hypocrisy is made all the more potent when, after the Turkish leader's galley-slaves and soldiers have all been massacred in an explosion of gunpowder (also created by Barabas), the Christians then take the remaining Turks prisoner in Malta, just as Barabas would have done—and the governor states that they should give thanks to Heaven as a result. The ending refuses to allow any group in the play to emerge blameless.