Appearances and Reality
One of the central themes in The Jew of Malta is the differences between what is real and what only appears real. For instance, Ferneze suggests that in taking all of Barabas' wealth, he is not at fault, but only fulfilling the curse of the Jews' inherited sin (Matthew 27:25). But Ferneze uses religion when it is convenient. He ignores the Christian admonition of kindness toward all men, and he lacks any compassion for the Jews. When he needs money, the Jews are suddenly outsiders, although there is every evidence that the governor has made use of the Jews when he needed their financial assistance. But Ferneze is not alone in his deception. The friars pretend to be pious when all they really want is Barabas' money. But Barabas is the most accomplished at deception, pretending to be outraged and destitute at the governor's confiscation of his property, but when alone, dealing matter-of-factly with the events, since he still has plenty of money hidden away. Barabas also pretends to both Lodowick and Mathias that Abigail shall belong to both young men. He pretends to befriend them, when he is really plotting their deaths. He also pretends to the friars that he will convert, setting them against one another, and he even pretends to the Turks that he is their friend, when he plans to murder them all. Barabas is a master at deception, but in reality, he is little different than the other characters—only more willing to kill his victims, rather than rob them.

Betrayal
The most significant betrayal in this play is found within the relationship between father and daughter. Abigail loves her father enough that she consents to a deception of the nuns, so that she can retrieve his hidden wealth. But Barabas betrays his daughter when he plots to destroy the man she loves. Mathias has done nothing to injure Barabas, but he is useful because he is both Lodowick's friend and Abigail's suitor. Barabas thinks that Mathias can be sacrificed because he is a Christian and so has no value to Barabas. But in murdering the young man, he betrays his daughter's implied trust that a father would not deliberately injure his daughter. When Abigail is dying, she thinks only of saving her father. She tells a friar of her father's murder of the young men—not to injure him, since the priest is obligated to keep the secret by the sanctity of his office—but to try and save him. She still loves her father, not knowing that he has deliberately poisoned her. There are lesser betrayals, such as that of Ithamore, who betrays his master because of lust for Bellamira, but none of the other betrayals are as significant as Barabas' betrayal of his daughter's love.

Greed
Almost every character in The Jew of Malta is motivated by greed. Barabas has more than enough money. He could easily have given half his estate to the governor and still had more than enough, but he wanted all that he had and even more. Ferneze, too, wants even more money. He is not willing to sacrifice to pay the tribute to the Turks, but, instead, wants to take the money from the Jews, and not content with half, he demands all of Barabas' wealth. Calymath's father has waited ten years to demand his tribute, not because he had forgotten about the money, but because he felt that by letting the tribute accumulate, the citizens of Malta would be unable to pay the tribute, and he could seize everything. Ithamore is promised one half of Barabas' estate, as his heir, but he is not content to wait and keeps increasing his blackmail demands for more and more money. Pilia-Borza and Bellamira are also motivated by greed to try first to steal and then later to blackmail money from Barabas. The friars, too, are motivated more by greed than piety in their attempt to convert Barabas. The need for more and more money has infected almost everyone in Malta.

Moral Corruption
Marlowe's Elizabethan audience would have automatically expected the Catholics to be depicted as corrupt. Corrupt friars have a long-standing literary tradition going back to Geoffrey Chaucer, and Marlowe's friars fit neatly into this tradition. The two squabble about who will have the privilege of saving Barabas' soul, but neither one is really interested in the Jew's eternal salvation. Barabas' repentance will come with his wealth, and each sees this wealth as a benefit to his own order. By the end of the play, Barabas has himself become corrupt. Throughout most of the play, he has been guided by revenge, dispatching most of his victims because they threaten him. But in the final act, he has achieved nearly everything he set out to do. Ferneze has been imprisoned; the rest of Barabas' enemies are all dead, and Barabas is the governor of the island. But then he sets out to methodically kill all the Turks, who have helped him accomplish all that he desired. Barabas has won, but he has enjoyed all the intrigue and the murder, and he does not wish to stop. He betrays his own motives in this final onslaught and is himself killed, corrupted by his own lack of moral guidance.

Prejudice
The stereotyping of Barabas and his general treatment by the Christians of Malta reflect Elizabethan ideas about Jews. There are references to Barabas' nose (evidently the actor playing this role wore a large false nose) and to Christian myths about Jews: they poison wells, kill sick people, murder at will, and cheat honest Christians out of their money. But there are also stereotypes about Catholics included in the text: their piety is false, nuns and priests engage in illicit sexual affairs, and they care more about money than the souls of their flock. As is the case with the Jews, the stereotypes about Catholics reflect the general Elizabethan fears about Catholics, whom they suspect of constantly trying to sell their country to the Pope in Rome.