Alithea Binnie (Tilda Swinton)is a British scholar who occasionally suffers from bizarre hallucinations of demonic beings. During a trip to Istanbul, Alithea purchases an antique bottle, and accidentally unleashes a Djinn (Idris Elba) that was trapped within it.

The Djinn offers to grant Alithea three wishes, so long as each one is truly her heart's desire, but Alithea argues that wishing is a mistake, accusing the Djinn of being a trickster.

In response to her accusation, the Djinn proceeds to tell her three tales of his past and how he ended up trapped in the bottle. The Djinn tells the story of the Queen of Sheba, his cousin and lover, being wooed by King Solomon, who imprisons the Djinn in a bottle to keep Sheba for himself.

The Djinn's second story centers on Gülten, a young concubine in the palace of Suleiman the Magnificent. After finding the Djinn's bottle, Gülten wishes for Suleiman's son, Mustafa, to fall in love with her and subsequently wishes to bear his child.

A favored concubine of Suleiman schemes to have her son on the throne so she seeds Suleiman's mind with the idea that Mustafa will conduct a coup against him and he is too weak to lead the kingdom. The Djinn tries to warn Gulten but being naive and ignorant with the dirty politics within the ruling class, she ignores him.

This result in Mustafa's murder, causing Gülten to leave behind the Djinn's hidden bottle and flee. Despite the Djinn's attempts to pursue and save her, the pregnant Gülten is also killed on Suleiman's orders before she can make her final wish.

The Djinn wanders the palace for over 100 years, invisible and intangible due to the concealment of the bottle. Meanwhile, the bottle is almost found by young princes Murad IV and Ibrahim, but they are unable to successfully uncover the bottle.

Years later, Murad IV goes into war, where he becomes a vicious and ruthless ruler, later dying from alcoholism. Ibrahim develops a fetish for voluptuous concubines and becomes the new sultan. His favorite among them, Sugar Lump, accidentally retrieves the bottle, whereupon the Djinn appears to her and desperately begs her to make a wish. Sugar Lump, being silly and terrified, thinking him to be a tricker and wishes for the Djinn to return to his bottle and for the bottle to be cast into the sea.

In the Djinn's final story, he tells of Zefir, the young wife of a Turkish merchant, who is gifted the bottle after it is recovered in the mid-19th century. Zefir wishes first for knowledge, which the Djinn grants in the form of literature, and later to perceive the world as djinns do.

Despite the Djinn's growing affection for Zefir and the fact she is now pregnant with his child, she grows increasingly crowded by his presence and her newfound knowledge. The Djinn offers to reside in his bottle whenever she wishes, but as he begins his return to the bottle, Zefir wishes to forget she ever met the Djinn, leaving him imprisoned and unknown once again.

The Djinn's final story moves Alithea to the point where she wishes for Djinn and herself to fall in love, resulting in them having sex. Afterwards, the Djinn and Alithea travel back to London together.

One day, Alithea discovers that the Djinn is gradually becoming weaker due to the effects that the city's cell tower and satellite transmissions have when interacting with his supernatural physiology. She uses her second wish to get the severely ill Djinn to speak again, apologizes for using her wish to deny them the chance to fall in love naturally, and uses her third and final wish to set the Djinn free, so he is able to return to "The Realm of Djinn".

Though expecting never to see him again, the now-healthy Djinn visits Alithea three years later and periodically returns throughout her lifetime.