Ultimately, the novel deals with the interplay of good and evil, innocence and guilt, courage and cowardice, exploring such issues as the responsibility towards truth when authority would deny it, and the freedom of the spirit in an unfree world. Love and sensuality are also dominant themes in the novel.
Margarita's devotional love for the Master leads her to leave her husband, but she emerges victorious. Her spiritual union with the Master is also a sexual one. The novel is a riot of sensual impressions, but the emptiness of sensual gratification without love is emphatically illustrated in the satirical passages. However, the stupidity of rejecting sensuality for the sake of empty respectability is also pilloried in the figure of Nikolai Ivanovich who becomes Natasha's hog-broomstick.
The interplay of fire, water, destruction, and other natural forces provides a constant accompaniment to the events of the novel, as do light and darkness, noise and silence, sun and moon, storms and tranquility, and other powerful polarities. There is a complex relationship between Jerusalem and Moscow throughout the novel, sometimes polyphony, sometimes counterpoint.
The novel is heavily influenced by Goethe's Faust, and its themes of cowardice, trust, intellectual curiosity, and redemption are prominent. Part of its literary brilliance lies in the different levels on which it can be read, as hilarious slapstick, deep philosophical allegory, and biting socio-political satire critical of not just the Soviet system but also the superficiality and vanity of modern life in general – jazz is a favourite target, ambivalent like so much else in the book in the fascination and revulsion with which it is presented. But the novel is also full of modern amenities like the model asylum, radio, street and shopping lights, cars, lorries, trams, and air travel. There is little evident nostalgia for any "good old days" – in fact, the only figure in the book to even mention Tsarist Russia is Satan himself. In another of its facets, perhaps showing a different aspect of Goethe's influence, the book is a Bildungsroman with Ivan Nikolayevich as its focus. Furthermore, there are strong elements of magic realism in the novel.