Who exactly was the black-winged deity of love? The secrets this masterpiece uncovers about the rogue genius

A young lad cries out while his skull is firmly held, a large thumb pressing into his cheek as his parent's powerful hand grasps him by the throat. That scene from The Sacrifice of Isaac appears in the Florentine museum, creating distress through the artist's chilling rendition of the suffering child from the scriptural account. The painting seems as if Abraham, commanded by God to kill his son, could break his neck with a solitary turn. Yet Abraham's preferred method involves the metallic steel knife he holds in his other palm, ready to slit Isaac's throat. One certain aspect remains – whomever posed as the sacrifice for this breathtaking piece demonstrated remarkable acting ability. There exists not only fear, surprise and pleading in his shadowed eyes but additionally profound grief that a protector could betray him so utterly.

The artist took a familiar biblical tale and transformed it so vibrant and visceral that its horrors appeared to happen directly in view of the viewer

Viewing in front of the artwork, viewers identify this as a real face, an accurate record of a young subject, because the same youth – recognizable by his tousled locks and almost dark pupils – features in two additional paintings by Caravaggio. In each case, that richly emotional visage commands the composition. In Youth With a Ram, he peers mischievously from the shadows while holding a lamb. In Amor Vincit Omnia, he grins with a toughness acquired on the city's streets, his black plumed appendages demonic, a unclothed adolescent running riot in a affluent dwelling.

Amor Vincit Omnia, currently displayed at a London museum, represents one of the most embarrassing artworks ever created. Observers feel totally disoriented gazing at it. Cupid, whose darts inspire people with often painful desire, is portrayed as a extremely real, vividly illuminated nude figure, standing over overturned objects that include stringed instruments, a musical score, metal armour and an architect's T-square. This heap of possessions resembles, intentionally, the mathematical and architectural gear strewn across the ground in the German master's print Melencolia I – except in this case, the melancholic mess is caused by this smirking deity and the mayhem he can unleash.

"Affection looks not with the eyes, but with the soul, / And thus is winged Cupid depicted blind," penned the Bard, just before this work was produced around the early 1600s. But Caravaggio's god is not unseeing. He stares directly at the observer. That countenance – sardonic and ruddy-faced, looking with brazen assurance as he struts unclothed – is the same one that screams in terror in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio painted his multiple images of the same unusual-appearing kid in the Eternal City at the dawn of the 17th century, he was the highly celebrated religious artist in a metropolis enflamed by Catholic renewal. The Sacrifice of Isaac reveals why he was sought to decorate sanctuaries: he could adopt a scriptural narrative that had been depicted numerous occasions previously and make it so fresh, so unfiltered and physical that the terror appeared to be occurring immediately in front of the spectator.

Yet there was another aspect to the artist, evident as quickly as he came in Rome in the winter that concluded 1592, as a painter in his initial 20s with no mentor or patron in the city, only skill and audacity. The majority of the works with which he caught the sacred city's eye were everything but holy. What may be the absolute earliest resides in London's art museum. A young man parts his crimson lips in a scream of pain: while stretching out his dirty digits for a cherry, he has rather been attacked. Youth Bitten by a Reptile is eroticism amid poverty: observers can discern Caravaggio's dismal room reflected in the cloudy waters of the transparent vase.

The adolescent sports a rose-colored flower in his coiffure – a symbol of the erotic trade in Renaissance art. Venetian painters such as Titian and Palma Vecchio portrayed courtesans grasping flowers and, in a painting lost in the second world war but documented through images, Caravaggio represented a famous woman courtesan, clutching a bouquet to her chest. The message of all these botanical indicators is obvious: sex for purchase.

What are we to interpret of the artist's sensual depictions of boys – and of a particular boy in specific? It is a question that has split his commentators ever since he achieved widespread recognition in the twentieth century. The complicated historical reality is that the artist was not the homosexual icon that, for example, Derek Jarman presented on film in his twentieth-century film Caravaggio, nor so completely devout that, as some art historians improbably assert, his Youth Holding Fruit is in fact a likeness of Jesus.

His initial works do offer overt sexual suggestions, or even propositions. It's as if Caravaggio, then a penniless young artist, identified with Rome's prostitutes, offering himself to survive. In the Florentine gallery, with this idea in consideration, viewers might turn to another initial work, the 1596 masterpiece Bacchus, in which the god of alcohol stares calmly at the spectator as he starts to untie the dark sash of his robe.

A few annums after Bacchus, what could have driven Caravaggio to paint Amor Vincit Omnia for the artistic collector the nobleman, when he was finally becoming nearly respectable with prestigious church commissions? This profane pagan deity revives the erotic challenges of his initial paintings but in a increasingly powerful, uneasy manner. Fifty years later, its secret seemed obvious: it was a representation of the painter's lover. A English traveller saw the painting in about 1649 and was informed its subject has "the physique and countenance of [Caravaggio's|his] owne boy or assistant that laid with him". The identity of this adolescent was Francesco.

The artist had been dead for about forty years when this story was recorded.