Who exactly was the black-winged deity of love? The secrets this masterwork reveals about the rebellious artist

The young lad screams as his head is forcefully gripped, a massive thumb pressing into his cheek as his father's mighty palm grasps him by the neck. This moment from The Sacrifice of Isaac visits the Uffizi Gallery, creating unease through Caravaggio's chilling rendition of the suffering child from the scriptural narrative. The painting seems as if the patriarch, instructed by the Divine to kill his offspring, could break his spinal column with a single twist. Yet Abraham's preferred method involves the metallic steel knife he holds in his other hand, prepared to slit Isaac's neck. One definite aspect stands out – whoever modeled as the sacrifice for this astonishing work demonstrated extraordinary acting ability. Within exists not only fear, shock and begging in his darkened gaze but also profound sorrow that a guardian could betray him so completely.

He adopted a well-known scriptural story and made it so vibrant and raw that its terrors appeared to unfold right in view of you

Viewing before the painting, viewers identify this as a real face, an precise depiction of a adolescent subject, because the identical boy – identifiable by his disheveled hair and nearly black pupils – appears in two other paintings by the master. In each case, that richly expressive face dominates the composition. In John the Baptist, he gazes mischievously from the shadows while embracing a lamb. In Victorious Cupid, he smirks with a hardness acquired on Rome's alleys, his dark feathery wings demonic, a naked adolescent running chaos in a affluent dwelling.

Amor Vincit Omnia, presently exhibited at a London gallery, constitutes one of the most discomfiting masterpieces ever created. Viewers feel completely unsettled looking at it. Cupid, whose arrows fill people with often painful desire, is portrayed as a extremely tangible, vividly lit unclothed form, standing over overturned objects that include stringed devices, a music manuscript, plate armour and an builder's T-square. This heap of possessions resembles, intentionally, the geometric and architectural equipment strewn across the ground in Albrecht Dürer's print Melancholy – save in this case, the melancholic mess is created by this grinning Cupid and the mayhem he can release.

"Affection sees not with the vision, but with the mind, / And therefore is winged Love depicted blind," wrote Shakespeare, just prior to this painting was produced around 1601. But Caravaggio's Cupid is not blind. He stares directly at the observer. That face – sardonic and ruddy-cheeked, staring with brazen assurance as he struts unclothed – is the identical one that screams in fear in Abraham's Test.

As the Italian master painted his multiple images of the identical unusual-looking kid in Rome at the dawn of the seventeenth century, he was the highly celebrated religious artist in a city ignited by Catholic renewal. Abraham's Offering reveals why he was commissioned to adorn sanctuaries: he could take a scriptural story that had been portrayed many occasions before and make it so new, so unfiltered and visceral that the horror appeared to be happening directly in front of the spectator.

Yet there existed a different side to the artist, evident as soon as he arrived in Rome in the winter that concluded the sixteenth century, as a artist in his initial 20s with no mentor or supporter in the city, only skill and boldness. The majority of the paintings with which he caught the holy metropolis's attention were everything but holy. That may be the very earliest hangs in London's National Gallery. A youth parts his crimson mouth in a yell of agony: while reaching out his dirty digits for a cherry, he has instead been bitten. Youth Bitten by a Reptile is sensuality amid squalor: viewers can discern Caravaggio's dismal room mirrored in the cloudy waters of the glass vase.

The boy sports a rose-colored flower in his coiffure – a emblem of the sex commerce in early modern painting. Northern Italian artists such as Titian and Palma Vecchio depicted prostitutes holding blooms and, in a painting destroyed in the second world war but known through photographs, the master represented a famous female prostitute, clutching a posy to her chest. The meaning of all these floral indicators is obvious: sex for sale.

What are we to make of the artist's erotic portrayals of youths – and of a particular boy in particular? It is a inquiry that has divided his interpreters ever since he gained widespread recognition in the 1980s. The complicated past reality is that the painter was not the queer hero that, for instance, Derek Jarman put on film in his twentieth-century movie about the artist, nor so entirely devout that, as certain artistic historians improbably claim, his Boy With a Basket of Fruit is in fact a likeness of Jesus.

His initial paintings indeed offer explicit erotic implications, or even propositions. It's as if Caravaggio, then a penniless youthful artist, identified with Rome's sex workers, offering himself to survive. In the Uffizi, with this idea in mind, observers might look to an additional early creation, the 1596 masterwork the god of wine, in which the god of wine stares coolly at the spectator as he begins to undo the black sash of his robe.

A few years after Bacchus, what could have driven Caravaggio to create Amor Vincit Omnia for the artistic collector the nobleman, when he was at last growing nearly established with prestigious ecclesiastical commissions? This profane pagan deity resurrects the erotic provocations of his early paintings but in a increasingly powerful, unsettling manner. Half a century afterwards, its hidden meaning seemed obvious: it was a portrait of Caravaggio's lover. A English visitor saw Victorious Cupid in about the mid-seventeenth century and was informed its subject has "the body & face of [Caravaggio's|his] owne youth or assistant that slept with him". The name of this adolescent was Cecco.

The painter had been dead for about forty annums when this account was recorded.