Who was the black-winged deity of love? What secrets that masterpiece reveals about the rogue genius

The youthful lad cries out while his skull is firmly gripped, a large digit digging into his face as his father's powerful hand holds him by the neck. This moment from The Sacrifice of Isaac appears in the Florentine museum, evoking distress through Caravaggio's harrowing rendition of the tormented child from the scriptural narrative. It appears as if Abraham, commanded by the Divine to sacrifice his son, could snap his neck with a single twist. Yet the father's preferred method involves the silvery steel blade he holds in his other hand, prepared to cut Isaac's neck. A certain element stands out – whomever posed as Isaac for this breathtaking work displayed extraordinary acting ability. Within exists not just fear, surprise and pleading in his shadowed gaze but additionally deep sorrow that a guardian could betray him so completely.

The artist took a well-known biblical story and transformed it so vibrant and visceral that its horrors seemed to unfold directly in view of the viewer

Viewing in front of the artwork, observers identify this as a actual countenance, an precise depiction of a young model, because the same boy – recognizable by his disheveled hair and nearly black pupils – appears in two other works by the master. In each instance, that highly emotional visage commands the composition. In John the Baptist, he peers playfully from the shadows while holding a lamb. In Victorious Cupid, he grins with a toughness acquired on the city's streets, his dark plumed appendages demonic, a naked child running riot in a well-to-do residence.

Victorious Cupid, presently displayed at a London museum, represents one of the most embarrassing masterpieces ever created. Viewers feel completely disoriented gazing at it. The god of love, whose arrows fill people with frequently agonizing desire, is portrayed as a very real, vividly illuminated nude figure, straddling toppled-over objects that include stringed devices, a music manuscript, metal armor and an builder's T-square. This heap of possessions echoes, intentionally, the geometric and construction equipment strewn across the floor in Albrecht Dürer's engraving Melancholy – save in this case, the melancholic disorder is caused by this smirking Cupid and the turmoil he can release.

"Affection sees not with the eyes, but with the soul, / And therefore is feathered Love depicted sightless," wrote Shakespeare, just prior to this work was produced around 1601. But the painter's Cupid is not blind. He stares straight at the observer. That face – sardonic and rosy-cheeked, staring with bold confidence as he poses unclothed – is the same one that screams in terror in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio created his three images of the same unusual-looking youth in the Eternal City at the dawn of the 17th century, he was the most celebrated sacred painter in a city ignited by religious renewal. The Sacrifice of Isaac reveals why he was commissioned to decorate churches: he could adopt a biblical story that had been depicted numerous occasions previously and render it so fresh, so raw and visceral that the terror seemed to be happening immediately before the spectator.

However there existed a different side to Caravaggio, evident as soon as he arrived in the capital in the cold season that concluded the sixteenth century, as a painter in his initial 20s with no teacher or patron in the city, just skill and audacity. Most of the works with which he caught the sacred city's attention were anything but holy. That could be the absolute first resides in London's National Gallery. A youth parts his crimson lips in a scream of agony: while reaching out his filthy fingers for a fruit, he has rather been attacked. Boy Bitten By a Lizard is eroticism amid poverty: observers can see the painter's gloomy chamber mirrored in the murky waters of the glass container.

The boy sports a pink flower in his hair – a symbol of the erotic trade in Renaissance art. Northern Italian artists such as Titian and Palma Vecchio portrayed courtesans grasping blooms and, in a painting lost in the WWII but documented through photographs, Caravaggio portrayed a famous female prostitute, clutching a posy to her chest. The message of all these botanical indicators is clear: intimacy for sale.

How are we to interpret of Caravaggio's sensual portrayals of youths – and of one boy in specific? It is a question that has divided his interpreters since he gained widespread recognition in the twentieth century. The complex historical reality is that the painter was not the queer icon that, for example, the filmmaker presented on film in his twentieth-century movie Caravaggio, nor so entirely pious that, as some artistic historians unbelievably assert, his Boy With a Basket of Fruit is actually a portrait of Christ.

His early works indeed make explicit erotic suggestions, or including propositions. It's as if the painter, then a penniless youthful creator, identified with the city's prostitutes, selling himself to live. In the Florentine gallery, with this idea in consideration, observers might turn to another initial work, the sixteenth-century masterwork the god of wine, in which the deity of wine stares coolly at you as he starts to undo the black ribbon of his robe.

A few years following the wine deity, what could have driven Caravaggio to create Amor Vincit Omnia for the artistic patron Vincenzo Giustiniani, when he was at last becoming almost established with prestigious church commissions? This unholy pagan god revives the sexual provocations of his initial works but in a more powerful, unsettling way. Half a century later, its secret seemed obvious: it was a representation of Caravaggio's companion. A English visitor viewed Victorious Cupid in about 1649 and was told its subject has "the physique and countenance of [Caravaggio's|his] own boy or assistant that laid with him". The identity of this adolescent was Cecco.

The painter had been dead for about 40 years when this story was documented.