What was the black-winged deity of love? What secrets this masterpiece uncovers about the rogue artist

The young boy screams as his skull is forcefully held, a massive digit pressing into his face as his father's mighty palm holds him by the neck. That moment from The Sacrifice of Isaac visits the Uffizi Gallery, evoking unease through the artist's harrowing portrayal of the suffering child from the biblical account. It appears as if Abraham, commanded by God to kill his son, could break his neck with a solitary turn. However Abraham's chosen approach involves the metallic steel blade he grips in his other palm, ready to slit Isaac's throat. A definite aspect remains – whomever modeled as Isaac for this astonishing piece displayed extraordinary acting skill. There exists not just dread, surprise and begging in his shadowed gaze but also deep sorrow that a guardian could abandon him so completely.

The artist adopted a familiar biblical story and made it so fresh and visceral that its terrors seemed to happen right in view of you

Viewing before the artwork, viewers identify this as a actual face, an accurate record of a young subject, because the identical youth – recognizable by his tousled hair and nearly black pupils – appears in several other paintings by Caravaggio. In every case, that highly expressive face dominates the scene. In John the Baptist, he gazes playfully from the shadows while embracing a ram. In Amor Vincit Omnia, he smirks with a toughness acquired on Rome's streets, his dark plumed appendages sinister, a naked child creating chaos in a well-to-do residence.

Amor Vincit Omnia, currently displayed at a London gallery, constitutes one of the most discomfiting artworks ever created. Viewers feel completely disoriented looking at it. Cupid, whose arrows fill people with often agonizing desire, is portrayed as a extremely tangible, vividly illuminated unclothed form, straddling toppled-over objects that comprise stringed instruments, a music manuscript, metal armor and an builder's T-square. This pile of possessions echoes, intentionally, the mathematical and construction equipment strewn across the ground in the German master's print Melancholy – save in this case, the melancholic mess is caused by this grinning Cupid and the mayhem he can release.

"Love looks not with the vision, but with the mind, / And therefore is feathered Love depicted sightless," penned Shakespeare, just before this work was produced around the early 1600s. But the painter's god is not blind. He gazes straight at the observer. That countenance – ironic and rosy-cheeked, staring with bold confidence as he struts naked – is the identical one that shrieks in terror in The Sacrifice of Isaac.

As Michelangelo Merisi da Caravaggio painted his three portrayals of the same distinctive-appearing youth in Rome at the start of the 17th century, he was the most acclaimed religious painter in a metropolis ignited by Catholic renewal. Abraham's Offering demonstrates why he was sought to decorate sanctuaries: he could take a biblical story that had been portrayed many occasions before and render it so new, so unfiltered and visceral that the terror seemed to be happening immediately before you.

Yet there existed a different side to Caravaggio, evident as soon as he arrived in Rome in the cold season that ended 1592, as a painter in his early 20s with no mentor or patron in the urban center, just talent and audacity. The majority of the works with which he caught the sacred metropolis's eye were anything but devout. What may be the absolute earliest hangs in London's National Gallery. A young man opens his red lips in a yell of pain: while reaching out his dirty fingers for a cherry, he has rather been attacked. Youth Bitten by a Reptile is eroticism amid poverty: viewers can discern Caravaggio's dismal chamber mirrored in the murky liquid of the glass container.

The boy sports a rose-colored blossom in his hair – a emblem of the erotic commerce in early modern art. Venetian artists such as Tiziano and Jacopo Palma portrayed courtesans holding flowers and, in a work destroyed in the WWII but known through photographs, Caravaggio portrayed a renowned woman 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 Caravaggio's erotic portrayals of youths – and of a particular adolescent in specific? It is a inquiry that has split his interpreters ever since he gained widespread recognition in the 1980s. The complex past truth is that the artist was not the homosexual hero that, for instance, Derek Jarman presented on screen in his twentieth-century film Caravaggio, nor so entirely devout that, as certain art historians improbably claim, his Youth Holding Fruit is actually a likeness of Jesus.

His early works indeed offer explicit sexual suggestions, or even propositions. It's as if Caravaggio, then a destitute youthful creator, aligned with Rome's prostitutes, offering himself to live. In the Florentine gallery, with this thought in mind, observers might turn to another early work, the 1596 masterwork Bacchus, in which the god of alcohol stares calmly at the spectator as he begins to untie the dark ribbon of his robe.

A few years following the wine deity, what could have driven the artist to create Amor Vincit Omnia for the art patron Vincenzo Giustiniani, when he was finally becoming almost respectable with important church commissions? This profane non-Christian deity revives the sexual challenges of his early paintings but in a increasingly powerful, unsettling manner. Half a century afterwards, its secret seemed clear: it was a representation of Caravaggio's lover. A British visitor viewed Victorious Cupid in about 1649 and was informed its subject has "the body & face of [Caravaggio's|his] owne youth or servant that laid with him". The identity of this adolescent was Francesco.

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